Pierrick Roger
| Snapshot Date: 2025-03-21 13:40 -0400 (Fri, 21 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: devel |
| git_last_commit: 686a27c |
| git_last_commit_date: 2024-10-29 11:04:36 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-22 11:43 -0400 (Sat, 22 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" | 4547 |
| 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: 2025-03-21 19:39:24 -0400 (Fri, 21 Mar 2025) |
| EndedAt: 2025-03-21 19:42:25 -0400 (Fri, 21 Mar 2025) |
| EllapsedTime: 181.7 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: x86_64-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 Monterey 12.7.6
* 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-x86_64/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: x86_64-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 [2025-03-21 19:40:27.653][biodb::testContext]
biodb.INFO [2025-03-21 19:40:27.657][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-21 19:40:27.658][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-03-21 19:40:27.660][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-21 19:40:27.661][biodb::testContext]
biodb.INFO [2025-03-21 19:40:27.669][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-21 19:40:27.672][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-21 19:40:27.680][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-21 19:40:27.682][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-21 19:40:27.683][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-21 19:40:27.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:27.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:27.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:27.688][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-21 19:40:27.712][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-21 19:40:27.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:27.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:27.715][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[2025-03-21 19:40:27.717][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-21 19:40:27.718][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-21 19:40:27.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:27.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:27.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:27.723][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-21 19:40:27.724][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-21 19:40:27.725][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-21 19:40:27.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:27.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:27.729][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[2025-03-21 19:40:27.730][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-21 19:40:27.732][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-21 19:40:27.733][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-21 19:40:27.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:27.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:27.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:27.737][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-21 19:40:27.739][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-21 19:40:27.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:27.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:27.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:27.744][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-21 19:40:27.745][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-21 19:40:27.746][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-21 19:40:27.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:27.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:27.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:27.750][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-21 19:40:27.751][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-21 19:40:27.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:27.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:27.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:27.755][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-21 19:40:27.756][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-21 19:40:27.757][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-21 19:40:27.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:27.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:27.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:27.761][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-21 19:40:27.762][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-21 19:40:27.763][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-21 19:40:27.764][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-21 19:40:27.765][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-21 19:40:27.766][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-21 19:40:27.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:27.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:27.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:27.771][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-21 19:40:27.772][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-21 19:40:27.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:27.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:27.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:27.776][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-21 19:40:27.778][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-21 19:40:27.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:27.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:27.781][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[2025-03-21 19:40:27.782][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-21 19:40:27.783][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-21 19:40:27.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:27.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:27.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:27.787][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-21 19:40:27.788][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-21 19:40:27.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:27.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:27.791][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[2025-03-21 19:40:27.792][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-21 19:40:27.793][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-21 19:40:27.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:27.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:27.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:27.798][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-21 19:40:27.799][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-21 19:40:27.822][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-21 19:40:27.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:27.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:27.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:27.828][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-21 19:40:27.829][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-21 19:40:27.830][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-21 19:40:27.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:27.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:27.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:27.838][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-21 19:40:27.881][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-21 19:40:27.909][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-21 19:40:27.910][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-21 19:40:27.912][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-21 19:40:27.914][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-21 19:40:27.915][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-21 19:40:27.916][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-21 19:40:27.917][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-21 19:40:27.918][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-21 19:40:27.920][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-21 19:40:27.921][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-21 19:40:27.922][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-21 19:40:27.923][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-21 19:40:27.924][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:40:27.925][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-21 19:40:27.926][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-21 19:40:27.926][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-21 19:40:27.926][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-21 19:40:27.926][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-21 19:40:27.926][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-21 19:40:27.927][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-21 19:40:27.928][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:40:27.929][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:40:27.930][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-21 19:40:27.931][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:40:27.932][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:40:27.933][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-21 19:40:27.934][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:40:27.935][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-21 19:40:27.936][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-21 19:40:27.938][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-21 19:40:27.939][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:40:27.941][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-21 19:40:27.943][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-21 19:40:27.944][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-21 19:40:27.945][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-21 19:40:27.947][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-21 19:40:27.948][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-21 19:40:27.949][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-21 19:40:27.950][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-21 19:40:27.951][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-21 19:40:27.952][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-21 19:40:27.953][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-21 19:40:27.954][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-21 19:40:27.955][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-21 19:40:27.956][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-21 19:40:27.957][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:40:27.958][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-21 19:40:27.959][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-21 19:40:27.959][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-21 19:40:27.959][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-21 19:40:27.959][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-21 19:40:27.959][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-21 19:40:27.960][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-21 19:40:27.962][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:40:27.962][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:40:27.964][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-21 19:40:27.965][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:40:27.966][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:40:27.967][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-21 19:40:27.967][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:40:27.968][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-21 19:40:27.969][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-21 19:40:27.970][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-21 19:40:27.972][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:40:27.973][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-21 19:40:27.975][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-21 19:40:27.976][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-21 19:40:27.977][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-21 19:40:27.978][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-21 19:40:27.979][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-21 19:40:27.980][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-21 19:40:27.981][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-21 19:40:27.982][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-21 19:40:27.983][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-21 19:40:27.984][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-21 19:40:27.985][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-21 19:40:27.987][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-21 19:40:27.988][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-21 19:40:27.989][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:40:27.990][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-21 19:40:27.991][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:40:27.992][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-21 19:40:27.993][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:40:27.994][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:40:27.996][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-21 19:40:27.997][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:40:27.998][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:40:27.999][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-21 19:40:28.000][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:40:28.001][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-21 19:40:28.002][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-21 19:40:28.003][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-21 19:40:28.005][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:40:28.006][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-21 19:40:28.008][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-21 19:40:28.009][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-21 19:40:28.010][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-21 19:40:28.012][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-21 19:40:28.013][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-21 19:40:28.015][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-21 19:40:28.016][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-21 19:40:28.017][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-21 19:40:28.018][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-21 19:40:28.020][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-21 19:40:28.021][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-21 19:40:28.022][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-21 19:40:28.023][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-21 19:40:28.025][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:40:28.026][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-21 19:40:28.027][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:40:28.028][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-21 19:40:28.029][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:40:28.031][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:40:28.032][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-21 19:40:28.033][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:40:28.034][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:40:28.035][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-21 19:40:28.037][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:40:28.038][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-21 19:40:28.039][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-21 19:40:28.040][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-21 19:40:28.041][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:40:28.045][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-21 19:40:28.046][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.071][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.DEBUG[2025-03-21 19:40:28.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.135][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".
biodb.DEBUG[2025-03-21 19:40:28.136][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-21 19:40:28.142][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-21 19:40:28.144][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-21 19:40:28.146][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-21 19:40:28.148][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-21 19:40:28.149][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-21 19:40:28.151][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-21 19:40:28.152][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-21 19:40:28.154][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-21 19:40:28.156][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-21 19:40:28.158][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-21 19:40:28.160][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-21 19:40:28.162][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-21 19:40:28.164][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-21 19:40:28.166][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-21 19:40:28.168][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-21 19:40:28.170][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-21 19:40:28.171][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-21 19:40:28.172][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-21 19:40:28.174][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-21 19:40:28.176][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-21 19:40:28.177][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-21 19:40:28.179][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-21 19:40:28.181][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-21 19:40:28.182][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-21 19:40:28.184][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-21 19:40:28.185][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-21 19:40:28.186][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-21 19:40:28.188][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-21 19:40:28.190][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-21 19:40:28.191][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-21 19:40:28.192][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-21 19:40:28.194][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-21 19:40:28.195][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-21 19:40:28.197][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-21 19:40:28.198][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-21 19:40:28.199][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-21 19:40:28.201][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-21 19:40:28.202][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-21 19:40:28.204][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-21 19:40:28.205][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-21 19:40:28.207][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-21 19:40:28.209][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-21 19:40:28.210][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-21 19:40:28.212][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-21 19:40:28.214][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-21 19:40:28.216][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-21 19:40:28.218][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-21 19:40:28.220][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-21 19:40:28.222][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-21 19:40:28.224][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-21 19:40:28.225][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-21 19:40:28.227][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-21 19:40:28.228][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-21 19:40:28.230][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-21 19:40:28.231][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-21 19:40:28.232][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-21 19:40:28.234][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-21 19:40:28.236][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-21 19:40:28.238][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-21 19:40:28.239][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-21 19:40:28.241][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-21 19:40:28.242][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-21 19:40:28.245][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-21 19:40:28.246][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-21 19:40:28.248][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-21 19:40:28.250][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-21 19:40:28.252][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-21 19:40:28.253][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-21 19:40:28.255][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-21 19:40:28.256][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-21 19:40:28.258][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-21 19:40:28.259][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-21 19:40:28.261][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-21 19:40:28.262][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-21 19:40:28.263][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-21 19:40:28.265][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-21 19:40:28.266][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-21 19:40:28.268][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-21 19:40:28.270][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-21 19:40:28.271][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-21 19:40:28.273][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-21 19:40:28.274][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-21 19:40:28.282][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-21 19:40:28.284][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-21 19:40:28.288][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-21 19:40:28.289][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.291][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.292][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.DEBUG[2025-03-21 19:40:28.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:28.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:28.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:28.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:28.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.322][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[2025-03-21 19:40:28.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:28.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:28.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.330][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.DEBUG[2025-03-21 19:40:28.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:28.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:28.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:28.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:28.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:28.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:28.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:28.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:28.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:28.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:28.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:28.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:28.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.375][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[2025-03-21 19:40:28.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:28.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:28.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:28.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:28.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:28.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:28.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:28.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:28.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:28.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:28.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:28.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:28.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:28.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:28.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:28.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:40:28.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:28.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:28.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.435][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.DEBUG[2025-03-21 19:40:28.437][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-21 19:40:28.450][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-21 19:40:28.452][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-21 19:40:28.453][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-21 19:40:28.454][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-21 19:40:28.456][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-21 19:40:28.457][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-21 19:40:28.458][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-21 19:40:28.459][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-21 19:40:28.460][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-21 19:40:28.461][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-21 19:40:28.462][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-21 19:40:28.463][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-21 19:40:28.464][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-21 19:40:28.465][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-21 19:40:28.466][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-21 19:40:28.466][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-21 19:40:28.466][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-21 19:40:28.466][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-21 19:40:28.466][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-21 19:40:28.466][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-21 19:40:28.466][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-21 19:40:28.466][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-21 19:40:28.466][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-21 19:40:28.466][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-21 19:40:28.466][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-21 19:40:28.468][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-21 19:40:28.469][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-21 19:40:28.469][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-21 19:40:28.469][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-21 19:40:28.470][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-21 19:40:28.471][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:40:28.472][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:40:28.474][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-21 19:40:28.475][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:40:28.475][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:40:28.476][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-21 19:40:28.477][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:40:28.477][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-21 19:40:28.478][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-21 19:40:28.480][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-21 19:40:28.481][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-21 19:40:28.483][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-21 19:40:28.483][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-21 19:40:28.493][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-21 19:40:28.495][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-21 19:40:28.497][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-21 19:40:28.498][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-21 19:40:28.500][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-21 19:40:28.502][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-21 19:40:28.532][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-21 19:40:28.533][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-21 19:40:28.539][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-21 19:40:28.545][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-21 19:40:28.585][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-21 19:40:28.587][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-21 19:40:28.588][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-21 19:40:28.589][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-21 19:40:28.599][biodb::testThat]
biodb.INFO [2025-03-21 19:40:28.600][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-03-21 19:40:28.601][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:40:28.602][biodb::testThat]
biodb.TRACE[2025-03-21 19:40:28.607][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-03-21 19:40:28.609][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:28.613][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:28.623][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:28.624][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:28.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:28.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:28.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:28.646][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:28.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:28.657][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:28.659][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:28.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.661][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:28.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:28.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.680][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:28.681][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:28.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.684][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.716][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:28.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:28.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.722][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:28.723][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:28.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.725][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.727][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:28.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:28.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.733][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:28.734][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:28.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.740][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.742][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:28.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:28.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.747][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:28.749][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:28.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.750][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.752][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:28.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:28.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.758][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:28.759][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:28.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.761][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.762][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:28.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:28.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.767][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:28.769][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:28.770][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.771][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.773][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:28.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:28.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.778][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:28.779][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:28.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.781][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:28.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:28.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.788][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:28.789][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:28.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.791][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.801][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:28.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:28.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.807][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:28.808][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:28.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.811][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.812][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:28.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:28.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.817][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:28.818][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:28.819][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.820][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.821][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:28.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:28.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:28.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:28.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:28.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:28.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:28.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:28.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:28.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:28.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:28.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:28.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:28.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:28.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:28.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:28.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:28.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:28.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:28.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:28.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:28.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:28.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:28.916][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-03-21 19:40:28.919][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:28.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:28.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.924][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:28.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:28.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.958][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:28.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:28.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.970][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:28.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:28.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.975][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:28.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:28.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:28.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:28.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.984][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-21 19:40:28.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-21 19:40:28.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.989][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-21 19:40:28.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-21 19:40:28.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:28.994][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-21 19:40:28.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-21 19:40:28.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:28.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.000][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-21 19:40:29.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-21 19:40:29.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.127][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.128][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.130][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.166][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.171][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.173][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.174][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.190][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:29.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:29.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.195][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:29.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:29.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.201][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:29.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:29.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.206][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:29.208][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:29.209][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.211][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.212][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:29.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:29.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.229][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:29.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:29.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.234][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:29.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:29.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.239][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:29.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:29.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.243][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:29.244][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:29.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.246][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.247][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:29.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:29.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:29.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:29.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.267][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:29.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:29.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:29.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:29.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.277][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:29.278][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:29.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.280][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:29.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:29.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:29.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:29.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:29.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:29.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.307][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:29.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:29.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.312][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:29.314][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:29.315][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.316][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:29.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:29.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.333][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:29.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:29.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.338][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:29.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:29.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.342][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:29.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:29.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.346][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:29.347][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:29.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.350][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.356][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:29.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:29.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.373][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-21 19:40:29.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:29.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.378][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-21 19:40:29.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:29.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.383][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-21 19:40:29.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:29.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.388][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-21 19:40:29.389][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:29.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.391][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.393][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-21 19:40:29.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:29.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.407][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:29.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:29.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.413][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:29.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:29.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.418][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:29.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:29.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.423][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:29.424][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:29.425][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.427][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.428][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:29.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:29.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.444][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:29.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:29.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.450][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:29.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:29.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.454][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:29.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:29.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.459][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:29.460][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:29.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.462][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.463][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:29.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:29.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.479][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:29.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:29.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.484][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:29.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:29.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.488][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:29.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:29.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.492][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:29.493][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:29.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.495][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.497][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:29.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:29.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.514][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:29.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:29.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.519][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:29.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:29.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.523][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:29.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:29.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.526][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:29.528][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:29.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.530][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.531][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:29.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:29.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.551][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.552][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.554][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.560][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:29.562][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:29.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.565][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.572][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:29.574][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:29.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.577][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.585][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:29.586][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:29.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.588][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.596][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:29.598][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:29.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.601][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.608][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:29.610][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:29.612][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.613][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.620][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:29.622][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:29.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.625][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.633][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:29.634][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:29.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.637][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.645][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-21 19:40:29.646][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:29.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.649][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.656][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:29.657][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:29.658][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.660][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.667][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:29.669][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:29.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.671][ef$get] fields variable is a list.
biodb.INFO [2025-03-21 19:40:29.683][biodb::testThat]
biodb.INFO [2025-03-21 19:40:29.685][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-21 19:40:29.686][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:40:29.688][biodb::testThat]
biodb.DEBUG[2025-03-21 19:40:29.708][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-03-21 19:40:29.716][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:29.722][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-03-21 19:40:29.724][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:40:29.726][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-03-21 19:40:29.728][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:29.769][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:29.771][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:29.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:29.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:29.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:29.783][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:29.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:29.785][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:29.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:29.790][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.791][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.792][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.793][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.822][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:29.824][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:29.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.827][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.829][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:29.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:29.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.835][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:29.836][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:29.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.838][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.840][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:29.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:29.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.844][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:29.846][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:29.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.848][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.849][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:29.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:29.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.853][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:29.855][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:29.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.857][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.859][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:29.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:29.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.864][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:29.865][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:29.866][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.867][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.869][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:29.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:29.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.873][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:29.874][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:29.876][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.877][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.878][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:29.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:29.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.884][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:29.885][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:29.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.887][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:29.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:29.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.893][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:29.894][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:29.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.896][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.897][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:29.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:29.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.902][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:29.904][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:29.905][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.906][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.908][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:29.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:29.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.912][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:29.914][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:29.915][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.916][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.917][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:29.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:29.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.926][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:29.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:29.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:29.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:29.977][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-03-21 19:40:29.978][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-21 19:40:29.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-21 19:40:29.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-21 19:40:29.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-21 19:40:29.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:29.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-21 19:40:29.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-21 19:40:29.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:29.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-21 19:40:30.004][biodb::testThat]
biodb.INFO [2025-03-21 19:40:30.005][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-21 19:40:30.007][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:40:30.008][biodb::testThat]
biodb.TRACE[2025-03-21 19:40:30.013][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:30.014][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:30.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.016][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:30.018][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-03-21 19:40:30.056][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:30.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:30.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.063][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:30.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:30.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.068][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:30.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:30.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:30.078][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-03-21 19:40:30.084][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-21 19:40:30.113][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:40:30.144][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-21 19:40:30.145][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:40:30.147][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-21 19:40:30.180][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[2025-03-21 19:40:30.186][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:40:30.187][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-21 19:40:30.189][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:40:30.192][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-21 19:40:30.194][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-03-21 19:40:30.214][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:30.215][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:30.217][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.218][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.219][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:30.221][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:30.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.224][ef$get] fields variable is a list.
biodb.INFO [2025-03-21 19:40:30.230][biodb::testThat]
biodb.INFO [2025-03-21 19:40:30.231][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-03-21 19:40:30.233][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:40:30.234][biodb::testThat]
biodb.TRACE[2025-03-21 19:40:30.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:30.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:30.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.273][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:30.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:30.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.278][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:30.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:30.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:30.370][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[2025-03-21 19:40:30.375][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:40:30.377][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-21 19:40:30.379][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:40:30.381][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-03-21 19:40:30.407][biodb::testThat]
biodb.INFO [2025-03-21 19:40:30.409][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-03-21 19:40:30.410][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:40:30.411][biodb::testThat]
biodb.TRACE[2025-03-21 19:40:30.438][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:30.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:30.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.445][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:30.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:30.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.450][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:30.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:30.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.455][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:30.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:30.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.459][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:30.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:30.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.465][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:30.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:30.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.470][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-21 19:40:30.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-21 19:40:30.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.476][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-21 19:40:30.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-21 19:40:30.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.481][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-21 19:40:30.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-21 19:40:30.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.486][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-21 19:40:30.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-21 19:40:30.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.522][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:30.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:30.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.528][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:30.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:30.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.534][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:30.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:30.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:30.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:30.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.544][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:30.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:30.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:30.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:30.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.555][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-21 19:40:30.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-21 19:40:30.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.560][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-21 19:40:30.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-21 19:40:30.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.565][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-21 19:40:30.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-21 19:40:30.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:30.570][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-21 19:40:30.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-21 19:40:30.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:30.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-21 19:40:30.584][biodb::testThat]
biodb.INFO [2025-03-21 19:40:30.585][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-21 19:40:30.586][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:40:30.588][biodb::testThat]
biodb.INFO [2025-03-21 19:40:30.599][biodb::testThat]
biodb.INFO [2025-03-21 19:40:30.600][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-21 19:40:30.602][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:40:30.603][biodb::testThat]
biodb.INFO [2025-03-21 19:40:30.615][biodb::testThat]
biodb.INFO [2025-03-21 19:40:30.616][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-21 19:40:30.618][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:40:30.620][biodb::testThat]
biodb.DEBUG[2025-03-21 19:40:30.625][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-03-21 19:40:31.575][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-03-21 19:40:32.722][biodb::testThat]
biodb.INFO [2025-03-21 19:40:32.724][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-21 19:40:32.726][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:40:32.727][biodb::testThat]
biodb.DEBUG[2025-03-21 19:40:33.093][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[2025-03-21 19:40:33.460][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:33.461][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:33.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:33.464][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:33.466][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:33.467][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:33.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:33.470][ef$get] fields variable is a list.
biodb.INFO [2025-03-21 19:40:33.473][biodb::testThat]
biodb.INFO [2025-03-21 19:40:33.474][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2025-03-21 19:40:33.476][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:40:33.477][biodb::testThat]
biodb.TRACE[2025-03-21 19:40:33.495][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:33.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:33.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:33.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:33.518][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:33.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:33.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:33.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:33.523][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:33.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:33.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:33.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:33.632][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[2025-03-21 19:40:33.637][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:40:33.639][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-21 19:40:33.641][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:40:33.643][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-21 19:40:33.739][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[2025-03-21 19:40:33.744][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:40:33.746][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-21 19:40:33.748][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:40:33.750][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-03-21 19:40:33.772][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-21 19:40:33.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-21 19:40:33.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:33.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:33.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:33.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:33.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:33.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:33.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:33.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:33.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:33.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:33.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:33.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:33.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:33.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:33.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:33.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:33.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:33.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:33.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:33.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:33.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:33.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:33.828][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[2025-03-21 19:40:33.833][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:40:33.835][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-21 19:40:33.837][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:40:33.840][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-21 19:40:33.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:33.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:33.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:33.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:33.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:33.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:33.856][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[2025-03-21 19:40:33.857][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-03-21 19:40:33.923][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:33.925][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-03-21 19:40:33.927][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:40:33.929][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:40:33.931][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:33.932][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:40:33.934][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:40:33.942][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:40:33.946][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:33.948][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:33.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:33.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:33.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:33.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:33.960][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[2025-03-21 19:40:33.962][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-03-21 19:40:33.965][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:40:33.967][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:40:33.968][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-03-21 19:40:39.343][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-03-21 19:40:39.701][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:40:39.704][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-03-21 19:40:39.726][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-03-21 19:40:39.730][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-03-21 19:40:39.733][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:40:39.735][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:39.737][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:39.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:39.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:39.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:39.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:39.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:39.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:39.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:39.756][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:39.758][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:39.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.760][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:39.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:39.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.766][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:39.768][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:39.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.770][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.772][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:39.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:39.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.778][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:39.779][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:39.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.781][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.783][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:39.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:39.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.788][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:39.789][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:39.791][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.792][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.794][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:39.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:39.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.799][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:39.800][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:39.801][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.803][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.811][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:39.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:39.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.822][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:39.824][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:39.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.826][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.828][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:39.829][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:39.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.831][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.832][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:39.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:39.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.838][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:39.839][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:39.841][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.842][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:39.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:39.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.849][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:39.850][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:39.851][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.852][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.854][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:39.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:39.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.859][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:39.861][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:39.862][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.863][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.865][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:39.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:39.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.870][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:39.871][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:39.872][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.873][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.874][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:39.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:39.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.879][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:39.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:39.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:39.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:39.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:39.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:39.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:39.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:39.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:39.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:39.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:39.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:39.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:39.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:39.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:39.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:39.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:39.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:39.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:39.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:39.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:39.930][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-03-21 19:40:39.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:39.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:39.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.965][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:39.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:39.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:39.971][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:39.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:39.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:39.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:39.980][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[2025-03-21 19:40:39.984][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:40:39.986][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-21 19:40:39.988][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:40:39.991][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-21 19:40:40.012][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:40.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:40.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:40.022][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:40.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:40.025][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:40.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:40.028][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:40.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:40.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:40.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:40.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:40.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:40.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:40.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:40.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:40.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:40.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:40.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:40.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:40.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:40.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:40.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:40.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:40.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:40.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:40.061][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-03-21 19:40:40.063][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:40.065][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-03-21 19:40:40.066][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:40:40.068][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:40:40.069][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:40.071][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:40:40.072][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:40:40.073][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:40:40.098][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:40.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:40.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:40.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:40.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:40.112][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:40.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:40.115][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-03-21 19:40:40.138][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:40:40.139][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:40:40.162][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-03-21 19:40:40.524][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-03-21 19:40:41.121][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:40:41.124][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-03-21 19:40:41.128][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-03-21 19:40:41.132][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-03-21 19:40:41.133][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:40:41.135][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:41.137][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:41.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:41.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:41.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:41.147][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:41.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:41.149][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:41.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:41.153][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:41.154][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:41.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.156][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:41.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:41.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.162][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:41.169][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:41.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.175][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.177][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:41.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:41.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.183][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:41.184][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:41.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.186][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.188][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:41.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:41.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.193][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:41.195][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:41.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.198][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.199][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:41.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:41.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.205][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:41.206][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:41.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.208][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.209][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:41.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:41.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.215][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:41.216][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:41.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.219][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.220][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:41.222][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:41.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.224][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.225][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:41.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:41.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.229][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:41.230][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:41.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.232][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:41.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:41.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.242][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:41.243][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:41.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.245][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.247][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:41.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:41.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.253][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:41.254][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:41.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.257][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.258][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:41.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:41.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.263][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:41.265][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:41.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.267][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.269][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:41.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:41.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:41.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:41.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:41.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:41.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:41.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:41.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:41.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:41.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:41.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:41.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:41.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:41.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:41.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:41.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:41.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:41.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:41.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:41.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:41.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:41.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:41.330][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-03-21 19:40:41.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:41.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:41.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.336][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:41.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:41.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:41.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:41.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:41.370][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[2025-03-21 19:40:41.373][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:40:41.375][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-21 19:40:41.376][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:40:41.377][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-21 19:40:41.380][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:41.382][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:41.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:41.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:41.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:41.391][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:41.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:41.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:41.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:41.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:41.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:41.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:41.404][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:41.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:41.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:41.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:41.409][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:41.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:41.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:41.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:41.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:41.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:41.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:41.424][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-03-21 19:40:41.459][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:41.462][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-03-21 19:40:41.487][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:40:41.489][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:40:41.492][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:41.494][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:40:41.496][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:40:41.499][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:40:41.503][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:41.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:41.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:41.513][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:41.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:41.516][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:41.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:41.519][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-03-21 19:40:41.523][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:40:41.524][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:40:41.526][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-03-21 19:40:41.888][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-03-21 19:40:42.240][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:40:42.243][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-03-21 19:40:42.247][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-03-21 19:40:42.251][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-03-21 19:40:42.253][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:40:42.255][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:42.257][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:42.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:42.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:42.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:42.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:42.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:42.272][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:42.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:42.276][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:42.277][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:42.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.280][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:42.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:42.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.287][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:42.288][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:42.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.291][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.292][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:42.293][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:42.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.295][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.297][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:42.299][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:42.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.302][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.303][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:42.305][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:42.306][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.307][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.308][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:42.310][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:42.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.312][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.314][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:42.315][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:42.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.318][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.320][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:42.321][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:42.323][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.325][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.326][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:42.328][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:42.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.331][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.333][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:42.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:42.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.339][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:42.352][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:42.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.355][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.358][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:42.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:42.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.364][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:42.365][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:42.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.368][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:42.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:42.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:42.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:42.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:42.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:42.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.385][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:42.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:42.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:42.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:42.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:42.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:42.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:42.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:42.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:42.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:42.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:42.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:42.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:42.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:42.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:42.425][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-03-21 19:40:42.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:42.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:42.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.431][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:42.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:42.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.436][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:42.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:42.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.441][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:42.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:42.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:42.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:42.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:42.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:42.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:42.453][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:42.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:42.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:42.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:42.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:42.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:42.468][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.DEBUG[2025-03-21 19:40:42.469][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-03-21 19:40:42.471][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:42.473][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-03-21 19:40:42.475][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:40:42.476][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:40:42.478][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:42.479][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:40:42.480][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:40:42.482][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:40:42.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:42.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:42.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:42.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:42.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:42.505][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:42.506][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[2025-03-21 19:40:42.508][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-03-21 19:40:42.512][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:40:42.513][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:40:42.515][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-03-21 19:40:42.883][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-03-21 19:40:43.238][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:40:43.241][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-03-21 19:40:43.247][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-03-21 19:40:43.251][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-03-21 19:40:43.254][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:40:43.256][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:43.257][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:43.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:43.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:43.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:43.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:43.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:43.272][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:43.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:43.277][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:43.279][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:43.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.281][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:43.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:43.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.287][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:43.288][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:43.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.290][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.292][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:43.293][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:43.295][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.295][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.298][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:43.299][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:43.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.302][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.303][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:43.304][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:43.306][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.307][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.308][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:43.310][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:43.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.312][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.313][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:43.315][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:43.316][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.317][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.318][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:43.320][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:43.321][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.322][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.324][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:43.325][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:43.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.327][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.329][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:43.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:43.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.335][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:43.336][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:43.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.339][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.340][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:43.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:43.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.345][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:43.346][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:43.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.348][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:43.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:43.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.367][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:43.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:43.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:43.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:43.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.377][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:43.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:43.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:43.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:43.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:43.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:43.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:43.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:43.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:43.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:43.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:43.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:43.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:43.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:43.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:43.415][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-03-21 19:40:43.416][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:43.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:43.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:43.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:43.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.425][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:43.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:43.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:43.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:43.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:43.436][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:43.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:43.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:43.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:43.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:43.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:43.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:43.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:43.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:43.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:43.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:43.455][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-03-21 19:40:43.456][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:43.458][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-03-21 19:40:43.460][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:40:43.461][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:40:43.462][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:43.464][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:40:43.465][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:40:43.466][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:40:43.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:43.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:43.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:43.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:43.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:43.480][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:43.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:43.482][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-03-21 19:40:43.486][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:40:43.493][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:40:43.496][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-03-21 19:40:43.861][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-03-21 19:40:44.213][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:40:44.231][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-03-21 19:40:44.274][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-03-21 19:40:44.286][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-03-21 19:40:44.289][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:40:44.291][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:44.292][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:44.295][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:44.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:44.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:44.303][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:44.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:44.306][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:44.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:44.311][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:44.312][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:44.313][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.314][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:44.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:44.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.321][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:44.322][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:44.323][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.324][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.326][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:44.326][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:44.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.329][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.331][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:44.332][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:44.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.334][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.336][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:44.337][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:44.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.339][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.340][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:44.342][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:44.343][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.344][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.345][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:44.347][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:44.348][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.349][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.351][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:44.352][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:44.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.354][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.356][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:44.358][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:44.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.360][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.362][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:44.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:44.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.366][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:44.368][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:44.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.370][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.371][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:44.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:44.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.377][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:44.378][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:44.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.381][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:44.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:44.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:44.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:44.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:44.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:44.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.407][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:44.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:44.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:44.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:44.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:44.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:44.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:44.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:44.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:44.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:44.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:44.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:44.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:44.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:44.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:44.442][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-03-21 19:40:44.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:44.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:44.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:44.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:44.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.453][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:44.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:44.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.458][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:44.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:44.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:44.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:44.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:44.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:44.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:44.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:44.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:44.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:44.478][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:44.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:44.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:44.483][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[2025-03-21 19:40:44.484][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-03-21 19:40:44.486][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:44.488][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-03-21 19:40:44.490][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:40:44.491][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:40:44.492][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:44.494][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:40:44.495][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:40:44.496][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:40:44.499][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:44.500][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:44.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:44.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:44.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:44.513][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:44.514][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[2025-03-21 19:40:44.516][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-03-21 19:40:44.520][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:40:44.521][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:40:44.524][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-03-21 19:40:44.883][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-03-21 19:40:45.243][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:40:45.246][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-03-21 19:40:45.262][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-03-21 19:40:45.266][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-03-21 19:40:45.269][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:40:45.270][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:45.271][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:45.274][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:45.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:45.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:45.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:45.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:45.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:45.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:45.290][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:45.292][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:45.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.294][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:45.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:45.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.300][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:45.302][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:45.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.304][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.306][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:45.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:45.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.312][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:45.313][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:45.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.315][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.318][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:45.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:45.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.323][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:45.324][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:45.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.327][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.329][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:45.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:45.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.334][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:45.335][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:45.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.337][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.339][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:45.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:45.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.344][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:45.345][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:45.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.347][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.348][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:45.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:45.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.354][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:45.355][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:45.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.357][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.359][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:45.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:45.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.365][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:45.366][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:45.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.369][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:45.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:45.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.376][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:45.377][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:45.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.379][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.381][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:45.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:45.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.387][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:45.389][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:45.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.398][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.401][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:45.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:45.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.406][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:45.407][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:45.409][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.410][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.412][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:45.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:45.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:45.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:45.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:45.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:45.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:45.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:45.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:45.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:45.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:45.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:45.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:45.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:45.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:45.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:45.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:45.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:45.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:45.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:45.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:45.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:45.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:45.467][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-03-21 19:40:45.469][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:45.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:45.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:45.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:45.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:45.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:45.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:45.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:45.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:45.483][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:45.484][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:45.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:45.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:45.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:45.495][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:45.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:45.498][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-03-21 19:40:45.500][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:45.502][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-03-21 19:40:45.504][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:40:45.505][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:40:45.507][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:45.508][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:40:45.510][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:40:45.511][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:40:45.514][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:45.515][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:45.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:45.522][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:45.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:45.532][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:45.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:45.535][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-03-21 19:40:45.539][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:40:45.540][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:40:45.542][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-03-21 19:40:45.917][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-03-21 19:40:46.275][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:40:46.278][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-03-21 19:40:46.283][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-03-21 19:40:46.287][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-03-21 19:40:46.290][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:40:46.291][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:46.293][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:46.296][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:46.297][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:46.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:46.305][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:46.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:46.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:46.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:46.312][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:46.313][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:46.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.315][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:46.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:46.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.322][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:46.323][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:46.324][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.326][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.327][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:46.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:46.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.332][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:46.333][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:46.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.335][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.337][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:46.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:46.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.342][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:46.343][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:46.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.346][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.347][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:46.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:46.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.351][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:46.353][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:46.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.355][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.357][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:46.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:46.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.362][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:46.364][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:46.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.366][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.368][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:46.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:46.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.372][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:46.373][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:46.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.375][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.377][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:46.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:46.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.383][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:46.384][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:46.386][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.387][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:46.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:46.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.405][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:46.407][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:46.408][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.409][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.411][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:46.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:46.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.415][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:46.417][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:46.418][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.419][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.421][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:46.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:46.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.426][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:46.428][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:46.429][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.430][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.432][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:46.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:46.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:46.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:46.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.444][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:46.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:46.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:46.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:46.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.453][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:46.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:46.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:46.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:46.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:46.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:46.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:46.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:46.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:46.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:46.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:46.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:46.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:46.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:46.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:46.490][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-03-21 19:40:46.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:46.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:46.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.497][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:46.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:46.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:46.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:46.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:46.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:46.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:46.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:46.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:46.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:46.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:46.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:46.518][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:46.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:46.521][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-03-21 19:40:46.522][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:46.524][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-03-21 19:40:46.533][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:40:46.535][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:40:46.537][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:46.539][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:40:46.540][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:40:46.542][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:40:46.546][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:46.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:46.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:46.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:46.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:46.558][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:46.559][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[2025-03-21 19:40:46.561][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-03-21 19:40:46.566][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:40:46.567][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:40:46.568][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-03-21 19:40:46.928][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-03-21 19:40:47.284][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:40:47.287][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-03-21 19:40:47.292][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-03-21 19:40:47.296][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-03-21 19:40:47.301][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:40:47.303][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:47.304][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:47.307][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:47.308][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:47.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:47.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:47.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:47.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:47.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:47.324][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:47.325][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:47.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.327][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:47.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:47.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.334][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:47.336][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:47.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.338][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.340][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:47.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:47.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.346][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:47.347][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:47.348][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.349][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.350][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:47.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:47.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.356][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:47.357][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:47.358][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.360][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.361][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:47.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:47.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.367][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:47.368][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:47.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.370][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.372][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:47.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:47.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.377][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:47.379][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:47.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.381][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.382][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:47.391][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:47.397][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.399][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.420][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:47.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:47.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.426][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:47.427][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:47.429][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.430][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.432][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:47.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:47.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.440][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:47.442][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:47.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.445][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.446][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:47.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:47.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.451][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:47.452][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:47.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.455][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.456][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:47.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:47.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.462][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:47.463][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:47.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.465][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.467][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:47.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:47.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.473][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:47.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:47.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:47.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:47.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:47.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:47.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:47.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:47.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:47.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:47.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:47.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:47.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:47.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:47.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:47.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:47.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:47.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:47.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:47.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:47.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:47.519][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-03-21 19:40:47.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:47.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:47.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.526][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:47.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:47.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:47.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:47.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:47.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:47.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:47.538][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:47.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:47.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:47.572][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:47.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:47.575][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:47.576][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[2025-03-21 19:40:47.577][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-03-21 19:40:47.578][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:47.580][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-03-21 19:40:47.582][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:40:47.583][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:40:47.584][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:47.585][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:40:47.585][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:40:47.586][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:40:47.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:47.589][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:47.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:47.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:47.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:47.601][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:47.603][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[2025-03-21 19:40:47.604][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-03-21 19:40:47.608][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:40:47.609][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:40:47.611][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-03-21 19:40:47.972][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-03-21 19:40:48.350][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:40:48.353][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-03-21 19:40:48.358][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-03-21 19:40:48.362][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-03-21 19:40:48.365][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:40:48.367][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:48.368][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:48.370][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:48.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:48.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:48.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:48.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:48.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:48.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:48.388][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:48.390][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:48.391][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.392][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:48.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:48.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.400][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:48.401][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:48.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.404][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.406][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:48.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:48.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.411][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:48.413][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:48.414][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.415][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.417][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:48.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:48.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.422][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:48.424][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:48.425][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.426][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.428][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:48.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:48.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.451][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:48.452][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:48.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.468][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.470][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:48.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:48.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.476][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:48.477][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:48.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.479][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.481][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:48.483][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:48.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.485][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.487][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:48.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:48.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.491][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:48.493][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:48.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.495][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:48.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:48.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.501][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:48.502][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:48.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.504][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.506][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:48.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:48.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.512][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:48.513][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:48.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.515][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.517][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:48.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:48.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.522][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:48.523][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:48.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.525][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.527][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:48.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:48.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:48.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:48.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:48.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:48.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:48.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:48.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:48.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:48.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:48.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:48.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:48.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:48.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:48.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:48.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:48.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:48.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:48.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:48.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:48.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:48.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:48.586][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-03-21 19:40:48.587][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:48.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:48.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.599][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:48.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:48.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:48.605][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:48.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:48.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:48.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:48.610][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:48.611][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:48.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:48.620][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:48.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:48.623][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:48.624][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[2025-03-21 19:40:48.625][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-03-21 19:40:48.627][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:48.629][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-03-21 19:40:48.631][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:40:48.632][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:40:48.634][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:48.635][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:40:48.636][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:40:48.637][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:40:48.641][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:48.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:48.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:48.650][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:48.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:48.653][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:48.654][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[2025-03-21 19:40:48.656][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-03-21 19:40:48.660][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:40:48.661][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:40:48.663][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-03-21 19:40:49.013][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-03-21 19:40:49.371][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:40:49.374][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-03-21 19:40:49.379][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-03-21 19:40:49.382][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-03-21 19:40:49.384][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:40:49.386][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:49.388][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:49.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:49.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:49.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:49.399][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:49.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:49.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:49.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:49.406][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:49.408][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:49.409][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.410][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:49.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:49.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.417][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:49.418][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:49.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.420][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.422][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:49.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:49.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.426][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:49.427][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:49.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.429][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.431][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:49.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:49.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.449][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:49.450][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:49.452][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.453][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.454][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:49.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:49.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.460][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:49.461][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:49.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.463][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.464][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:49.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:49.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.469][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:49.470][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:49.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.472][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.474][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:49.475][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:49.476][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.478][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.479][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:49.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:49.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.483][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:49.485][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:49.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.487][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.489][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:49.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:49.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.494][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:49.495][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:49.497][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.498][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.500][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:49.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:49.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.505][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:49.506][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:49.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.508][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.510][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:49.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:49.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.515][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:49.516][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:49.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.519][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.520][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:49.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:49.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:49.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:49.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:49.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:49.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:49.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:49.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.540][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:49.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:49.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:49.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:49.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:49.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:49.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:49.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:49.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:49.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:49.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:49.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:49.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:49.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:49.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:49.583][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-03-21 19:40:49.584][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:49.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:49.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.590][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:49.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:49.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:49.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:49.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:49.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:49.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:49.600][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:49.601][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:49.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:49.609][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:49.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:49.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:49.613][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[2025-03-21 19:40:49.614][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-03-21 19:40:49.615][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:49.617][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-03-21 19:40:49.619][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:40:49.620][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:40:49.622][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:49.623][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:40:49.624][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:40:49.625][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:40:49.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:49.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:49.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:49.637][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:49.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:49.639][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:49.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:49.642][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-03-21 19:40:49.645][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:40:49.646][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:40:49.647][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-03-21 19:40:50.002][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-03-21 19:40:50.359][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:40:50.362][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-03-21 19:40:50.367][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-03-21 19:40:50.371][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-03-21 19:40:50.374][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:40:50.375][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:50.377][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:50.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:50.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:50.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:50.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:50.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:50.392][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:50.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:50.396][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:50.397][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:50.398][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.399][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:50.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:50.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.411][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:50.417][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:50.418][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.419][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.421][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:50.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:50.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.425][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:50.426][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:50.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.429][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.430][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:50.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:50.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.436][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:50.437][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:50.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.439][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.440][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:50.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:50.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.446][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:50.447][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:50.449][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.450][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.452][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:50.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:50.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.456][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:50.457][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:50.459][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.460][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.461][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:50.463][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:50.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.465][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.466][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:50.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:50.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.472][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:50.473][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:50.474][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.475][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:50.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:50.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.481][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:50.482][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:50.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.485][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.487][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:50.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:50.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.492][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:50.493][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:50.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.494][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.496][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:50.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:50.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.501][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:50.503][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:50.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.504][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.506][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:50.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:50.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.512][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:50.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:50.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:50.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:50.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:50.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:50.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:50.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:50.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:50.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:50.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:50.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:50.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:50.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:50.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:50.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:50.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:50.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:50.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:50.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:50.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:50.571][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-03-21 19:40:50.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:50.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:50.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.578][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:50.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:50.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:50.581][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:50.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:50.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:50.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:50.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:50.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:50.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:50.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:50.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:50.598][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:50.599][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[2025-03-21 19:40:50.601][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-03-21 19:40:50.602][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:50.604][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-03-21 19:40:50.606][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:40:50.607][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:40:50.608][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:50.610][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:40:50.611][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:40:50.612][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:40:50.616][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:50.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:50.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:50.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:50.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:50.626][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:50.627][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[2025-03-21 19:40:50.629][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-03-21 19:40:50.632][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:40:50.633][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:40:50.634][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-03-21 19:40:50.985][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-03-21 19:40:51.341][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:40:51.344][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-03-21 19:40:51.349][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-03-21 19:40:51.353][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-03-21 19:40:51.355][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:40:51.357][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:51.358][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:51.359][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:51.360][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:51.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:51.379][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:51.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:51.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:51.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:51.385][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:51.387][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:51.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.389][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:51.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:51.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.394][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:51.396][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:51.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.398][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.399][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:51.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:51.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.405][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:51.406][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:51.408][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.409][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.411][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:51.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:51.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.416][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:51.417][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:51.418][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.419][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.421][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:51.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:51.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.425][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:51.427][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:51.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.429][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.431][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:51.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:51.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.436][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:51.437][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:51.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.439][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.440][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:51.441][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:51.443][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.444][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.445][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:51.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:51.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.450][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:51.451][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:51.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.454][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:51.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:51.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.459][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:51.461][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:51.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.463][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.464][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:51.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:51.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.469][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:51.470][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:51.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.472][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.473][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:51.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:51.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.478][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:51.479][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:51.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.481][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.482][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:51.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:51.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:51.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:51.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:51.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:51.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:51.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:51.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.508][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:51.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:51.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:51.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:51.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:51.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:51.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:51.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:51.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:51.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:51.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:51.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:51.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:51.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:51.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:51.544][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-03-21 19:40:51.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:51.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:51.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:51.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:51.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:51.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:51.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:51.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:51.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:51.559][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:51.560][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:51.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:51.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:51.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:51.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:51.572][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.DEBUG[2025-03-21 19:40:51.573][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-03-21 19:40:51.575][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:51.577][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-03-21 19:40:51.578][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:40:51.580][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:40:51.581][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:51.582][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:40:51.583][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:40:51.584][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:40:51.588][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:51.589][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:51.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:51.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:51.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:51.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:51.601][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[2025-03-21 19:40:51.603][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-03-21 19:40:51.606][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:40:51.607][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:40:51.609][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-03-21 19:40:51.968][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-03-21 19:40:52.317][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:40:52.320][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-03-21 19:40:52.338][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-03-21 19:40:52.343][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-03-21 19:40:52.345][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:40:52.347][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:52.348][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:52.350][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:52.352][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:52.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:52.359][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:52.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:52.361][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:52.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:52.366][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:52.367][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:52.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.370][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:52.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:52.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.377][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:52.379][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:52.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.381][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.383][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:52.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:52.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.388][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:52.390][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:52.391][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.392][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.394][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:52.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:52.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.399][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:52.400][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:52.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.403][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.404][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:52.406][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:52.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.408][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.409][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:52.411][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:52.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.413][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.414][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:52.416][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:52.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.418][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.420][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:52.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:52.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.425][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:52.426][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:52.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.428][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:52.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:52.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.435][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:52.436][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:52.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.438][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.440][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:52.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:52.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.445][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:52.446][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:52.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.448][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.450][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:52.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:52.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.455][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:52.457][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:52.458][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.459][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:52.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:52.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:52.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:52.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:52.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:52.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:52.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:52.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:52.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:52.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:52.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:52.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:52.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:52.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:52.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:52.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:52.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:52.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:52.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:52.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:52.517][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-03-21 19:40:52.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:52.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:52.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.524][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:52.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:52.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:52.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:52.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:52.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:52.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:52.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:52.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:52.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:52.542][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:52.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:52.544][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:52.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:52.547][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-03-21 19:40:52.548][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:52.550][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-03-21 19:40:52.551][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:40:52.553][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:40:52.555][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:52.556][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:40:52.557][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:40:52.559][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:40:52.562][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:52.563][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:52.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:52.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:52.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:52.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:52.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:52.576][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-03-21 19:40:52.579][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:40:52.581][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:40:52.582][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-03-21 19:40:52.943][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-03-21 19:40:53.293][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:40:53.296][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-03-21 19:40:53.309][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-03-21 19:40:53.314][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-03-21 19:40:53.316][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:40:53.318][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:53.319][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:53.321][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:53.322][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:53.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:53.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:53.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:53.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:53.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:53.338][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:53.340][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:53.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.342][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:53.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:53.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.349][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:53.351][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:53.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.353][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.354][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:53.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:53.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.358][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:53.360][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:53.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.362][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.364][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:53.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:53.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.369][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:53.370][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:53.371][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.372][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.373][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:53.375][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:53.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.377][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.378][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:53.379][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:53.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.381][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.382][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:53.383][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:53.384][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.386][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.388][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:53.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:53.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.393][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:53.394][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:53.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.396][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.397][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:53.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:53.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.402][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:53.404][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:53.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.406][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.408][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:53.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:53.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.413][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:53.414][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:53.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.416][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.418][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:53.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:53.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.422][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:53.424][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:53.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.425][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.427][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:53.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:53.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:53.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:53.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:53.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:53.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:53.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:53.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:53.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:53.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:53.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:53.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:53.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:53.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:53.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:53.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:53.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:53.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:53.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:53.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:53.484][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-03-21 19:40:53.486][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:53.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:53.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:53.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:53.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:53.495][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:53.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:53.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:53.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:53.500][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:53.501][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:53.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:53.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:53.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:53.512][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:53.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:53.514][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-03-21 19:40:53.515][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:53.518][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-03-21 19:40:53.519][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:40:53.521][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:40:53.522][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:53.523][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:40:53.525][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:40:53.526][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:40:53.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:53.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:53.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:53.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:53.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:53.542][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:53.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:53.545][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-03-21 19:40:53.548][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:40:53.550][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:40:53.552][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-03-21 19:40:53.902][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-03-21 19:40:54.258][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:40:54.261][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-03-21 19:40:54.275][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-03-21 19:40:54.279][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-03-21 19:40:54.281][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:40:54.283][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:54.285][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:54.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:54.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:54.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:54.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:54.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:54.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:54.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:54.302][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:54.303][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:54.305][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.306][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:54.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:54.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.312][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:54.313][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:54.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.315][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.317][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:54.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:54.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.321][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:54.323][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:54.323][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.324][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.325][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:54.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:54.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.329][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:54.331][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:54.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.334][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.335][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:54.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:54.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.339][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:54.340][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:54.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.342][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.343][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:54.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:54.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.347][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:54.348][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:54.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.350][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.351][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:54.352][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:54.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.354][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.356][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:54.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:54.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.361][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:54.363][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:54.364][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.365][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:54.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:54.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.372][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:54.373][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:54.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.376][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.378][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:54.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:54.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.382][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:54.383][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:54.385][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.386][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.387][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:54.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:54.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.399][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:54.401][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:54.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.403][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.404][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:54.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:54.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:54.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:54.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:54.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:54.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:54.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:54.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:54.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:54.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:54.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:54.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:54.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:54.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:54.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:54.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:54.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:54.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:54.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:54.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:54.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:54.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:54.460][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-03-21 19:40:54.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:54.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:54.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.466][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:54.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:54.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:54.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:54.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:54.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:54.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:54.476][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:54.477][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:54.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:54.484][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:54.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:54.486][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:54.487][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[2025-03-21 19:40:54.489][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-03-21 19:40:54.490][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:54.492][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-03-21 19:40:54.493][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:40:54.495][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:40:54.496][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:54.497][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:40:54.498][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:40:54.499][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:40:54.503][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:54.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:54.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:54.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:54.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:54.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:54.516][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[2025-03-21 19:40:54.525][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-03-21 19:40:54.529][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:40:54.531][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:40:54.532][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-03-21 19:40:54.894][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-03-21 19:40:55.248][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:40:55.250][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-03-21 19:40:55.255][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-03-21 19:40:55.258][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-03-21 19:40:55.260][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:40:55.262][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:55.263][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:55.265][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:55.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:55.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:55.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:55.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:55.275][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:55.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:55.279][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:55.280][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:55.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.282][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:55.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:55.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.288][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:55.289][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:55.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.291][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.293][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:55.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:55.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.297][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:55.299][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:55.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.301][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.302][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:55.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:55.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.307][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:55.308][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:55.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.310][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.312][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:55.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:55.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.317][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:55.319][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:55.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.321][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.323][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:55.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:55.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.327][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:55.329][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:55.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.330][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.332][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:55.333][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:55.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.335][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.337][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:55.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:55.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.341][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:55.342][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:55.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.345][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:55.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:55.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.350][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:55.357][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:55.363][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.365][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.367][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:55.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:55.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.373][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:55.374][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:55.375][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.376][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.378][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:55.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:55.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.383][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:55.385][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:55.386][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.387][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.389][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:55.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:55.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:55.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:55.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:55.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:55.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:55.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:55.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:55.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:55.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:55.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:55.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:55.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:55.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:55.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:55.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:55.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:55.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:55.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:55.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:55.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:55.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:55.445][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-03-21 19:40:55.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:55.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:55.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:55.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:55.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:55.457][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:55.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:55.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:55.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:55.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:55.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:55.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:55.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:55.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:55.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:55.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:55.477][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-03-21 19:40:55.479][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:55.481][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-03-21 19:40:55.483][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:40:55.484][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:40:55.485][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:55.486][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:40:55.494][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:40:55.495][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:40:55.499][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:55.501][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:55.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:55.509][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:55.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:55.512][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:55.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:55.515][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-03-21 19:40:55.518][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:40:55.520][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:40:55.521][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-03-21 19:40:55.871][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-03-21 19:40:56.230][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:40:56.232][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-03-21 19:40:56.236][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-03-21 19:40:56.240][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-03-21 19:40:56.242][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:40:56.244][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:56.245][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:56.247][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:56.248][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:56.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:56.254][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:56.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:56.256][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:56.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:56.259][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:56.260][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:56.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.262][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:56.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:56.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.268][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:56.269][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:56.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.271][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.272][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:56.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:56.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.276][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:56.277][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:56.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.279][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.280][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:56.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:56.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.284][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:56.284][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:56.285][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.286][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.287][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:56.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:56.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.291][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:56.292][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:56.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.293][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.294][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:56.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:56.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.298][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:56.299][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:56.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.300][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.301][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:56.302][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:56.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.304][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.317][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:56.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:56.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.323][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:56.325][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:56.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.327][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:56.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:56.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.332][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:56.333][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:56.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.336][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.337][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:56.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:56.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.342][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:56.343][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:56.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.345][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.346][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:56.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:56.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.351][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:56.352][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:56.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.355][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.357][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:56.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:56.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:56.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:56.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:56.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:56.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:56.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:56.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:56.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:56.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:56.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:56.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:56.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:56.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:56.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:56.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:56.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:56.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:56.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:56.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:56.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:56.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:56.408][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-03-21 19:40:56.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:56.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:56.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.414][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:56.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:56.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:56.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:56.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:56.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:56.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:56.422][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:56.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:56.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:56.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:56.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:56.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:56.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:56.443][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-03-21 19:40:56.444][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:56.446][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-03-21 19:40:56.447][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:40:56.448][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:40:56.449][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:56.450][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:40:56.451][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:40:56.452][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:40:56.456][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:56.457][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:56.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:56.465][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:56.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:56.467][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:56.468][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.DEBUG[2025-03-21 19:40:56.470][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-03-21 19:40:56.473][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:40:56.474][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:40:56.475][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-03-21 19:40:56.838][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-03-21 19:40:57.196][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:40:57.199][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-03-21 19:40:57.205][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-03-21 19:40:57.209][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-03-21 19:40:57.212][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:40:57.214][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:57.216][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:57.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:57.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:57.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:57.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:57.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:57.233][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:57.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:57.238][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:57.239][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:57.241][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.242][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:57.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:57.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.249][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:57.251][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:57.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.253][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.255][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:57.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:57.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.261][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:57.262][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:57.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.265][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.266][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:57.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:57.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.272][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:57.274][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:57.275][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.277][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.278][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:57.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:57.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.284][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:57.285][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:57.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.298][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.300][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:57.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:57.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.306][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:57.306][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:57.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.308][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.309][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:57.311][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:57.312][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.313][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.315][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:57.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:57.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.320][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:57.322][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:57.323][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.324][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:57.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:57.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.331][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:57.332][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:57.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.335][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.336][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:57.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:57.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.341][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:57.343][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:57.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.345][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.347][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:57.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:57.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.353][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:57.354][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:57.355][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.356][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.357][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:57.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:57.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:57.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:57.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.367][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:57.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:57.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:57.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:57.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:57.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:57.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:57.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:57.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:57.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:57.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:57.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:57.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:57.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:57.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:57.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:57.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:57.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:57.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:57.408][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-03-21 19:40:57.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:57.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:57.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:57.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:57.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:57.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:57.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:57.448][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:57.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:57.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:57.460][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:57.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:57.462][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:57.463][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.DEBUG[2025-03-21 19:40:57.464][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-03-21 19:40:57.465][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:57.467][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-03-21 19:40:57.468][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:40:57.474][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml".
biodb.DEBUG[2025-03-21 19:40:57.476][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:57.478][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:57.480][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:57.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:57.484][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:57.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:57.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:57.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:57.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:57.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:57.501][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:57.502][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:57.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.505][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:57.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:57.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.512][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:57.513][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:57.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.515][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.516][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:57.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:57.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.520][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:57.522][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:57.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.523][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.525][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:57.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:57.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.531][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:57.532][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:57.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.534][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.536][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:57.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:57.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.539][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:57.541][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:57.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.543][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:57.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:57.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.549][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:57.549][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:57.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.551][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.552][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:57.554][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:57.555][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.556][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.557][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:57.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:57.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.569][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:57.571][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:57.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.573][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.575][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:57.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:57.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.578][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:57.579][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:57.580][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.581][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.583][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:57.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:57.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.587][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:57.588][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:57.589][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.589][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.591][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:57.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:57.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.596][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:57.597][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:57.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.598][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.600][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:57.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:57.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:57.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:57.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:57.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:57.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:57.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:57.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.617][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:57.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:57.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:57.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:57.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:57.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:57.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:57.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:57.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:57.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:57.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:57.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:57.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:57.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:57.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:57.644][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-03-21 19:40:57.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:57.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:57.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:57.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:57.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:57.651][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:57.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:57.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:57.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:57.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:57.656][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:57.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:57.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:57.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:57.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:57.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:57.672][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-03-21 19:40:57.673][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:57.675][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.INFO [2025-03-21 19:40:57.676][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-03-21 19:40:57.677][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:40:57.678][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:40:57.679][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:57.680][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:40:57.681][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:40:57.682][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:40:57.685][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:57.686][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:57.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:57.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:57.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:57.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:57.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:57.697][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-03-21 19:40:57.700][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:40:57.701][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:40:57.703][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-03-21 19:40:58.058][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-03-21 19:40:58.409][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:40:58.412][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-03-21 19:40:58.417][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-03-21 19:40:58.421][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-03-21 19:40:58.423][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:40:58.425][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:58.427][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:58.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:58.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:58.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:58.439][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:58.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:58.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:58.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:40:58.444][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:58.445][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:58.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.448][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:58.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:58.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.455][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:58.456][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:58.458][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.459][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.461][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:58.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:58.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.466][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:58.468][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:58.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.470][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.471][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:58.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:58.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.476][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:58.477][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:58.477][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.478][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.479][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:58.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:58.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.483][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:58.484][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:58.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.497][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.499][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:58.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:58.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.505][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:58.506][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:58.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.509][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.510][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:58.511][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:58.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.513][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.515][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:58.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:58.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.519][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:58.521][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:58.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.523][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:58.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:58.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.529][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:58.530][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:58.531][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.532][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.534][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:58.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:58.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.539][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:58.540][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:58.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.543][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.545][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:58.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:58.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.549][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:58.550][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:58.551][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.553][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.554][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:58.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:58.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:58.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:58.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:58.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:58.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:58.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:58.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:58.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:58.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:58.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:58.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:58.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:58.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:58.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:58.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:58.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:58.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:58.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:58.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:58.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:58.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:58.604][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-03-21 19:40:58.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:58.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:58.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.617][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:58.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:58.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:58.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:58.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:58.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:58.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:58.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:58.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:58.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:58.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:58.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:58.638][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:58.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:58.641][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-03-21 19:40:58.643][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:40:58.645][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-03-21 19:40:58.647][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:40:58.648][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:40:58.650][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:40:58.651][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:40:58.652][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:40:58.653][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:40:58.656][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:58.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:58.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:58.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:58.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:58.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:58.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:40:58.672][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-03-21 19:40:58.676][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:40:58.678][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:40:58.679][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-03-21 19:40:59.029][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-03-21 19:40:59.387][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:40:59.389][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-03-21 19:40:59.394][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-03-21 19:40:59.398][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-03-21 19:40:59.401][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:40:59.403][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:40:59.404][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:40:59.407][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:40:59.408][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:40:59.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:40:59.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:40:59.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:40:59.420][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:40:59.421][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.TRACE[2025-03-21 19:40:59.424][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:59.426][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:59.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.428][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:59.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:59.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.435][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:59.436][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:59.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.438][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.440][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:40:59.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:40:59.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.446][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:59.447][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:59.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.462][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.464][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:40:59.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:40:59.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.469][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:59.470][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:59.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.473][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.474][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:40:59.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:40:59.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.479][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:59.481][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:59.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.483][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.485][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:40:59.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:40:59.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.490][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:59.491][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:40:59.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.494][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.496][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:59.497][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:59.498][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.500][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.501][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:40:59.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:59.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.507][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:59.508][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:59.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.511][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:59.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:40:59.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.518][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:59.519][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:59.521][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.522][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.524][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:40:59.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:40:59.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.530][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:59.531][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:59.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.534][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.536][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:40:59.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:40:59.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.541][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:59.542][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:59.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.544][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.545][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:40:59.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:40:59.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:59.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:59.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:59.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:59.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:59.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:59.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:40:59.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:40:59.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:59.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:59.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:59.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:59.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:59.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:59.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:59.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:59.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:59.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:59.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:40:59.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:40:59.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:59.607][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-03-21 19:40:59.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:59.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:59.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:59.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:59.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:40:59.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:59.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:40:59.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:40:59.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:40:59.655][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:40:59.660][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:40:59.661][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:40:59.664][private$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[2025-03-21 19:41:00.168][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[2025-03-21 19:41:00.671][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2025-03-21 19:41:00.674][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-03-21 19:41:00.676][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-03-21 19:41:00.680][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-03-21 19:41:00.685][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:00.686][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:00.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:00.694][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:00.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:00.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:00.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:00.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:00.714][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:00.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:00.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:00.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:00.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:00.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:00.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:00.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.743][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.756][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:00.761][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:00.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:00.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:00.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:00.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:00.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:00.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:00.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:00.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:00.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:00.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:00.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:00.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:00.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:00.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:00.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.829][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:00.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:00.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:00.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:00.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:00.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:00.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:00.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:00.856][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.861][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:00.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:00.871][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:00.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:00.878][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:00.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:00.880][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:00.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:00.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:00.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:00.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:00.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:00.905][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:00.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:00.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:00.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:00.909][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:00.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:00.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:00.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:00.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:00.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:00.932][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:00.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:00.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.938][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:00.942][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:00.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:00.946][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:00.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:00.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:00.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:00.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:00.957][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:00.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:00.959][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:00.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:01.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:01.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:01.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:01.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:01.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:01.148][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:01.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:01.151][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.155][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.159][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:01.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:01.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:01.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:01.170][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:01.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:01.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:01.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:01.174][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.179][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.184][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:01.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:01.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:01.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:01.194][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:01.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:01.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:01.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:01.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.204][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.208][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:01.213][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:01.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:01.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:01.221][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:01.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:01.224][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:01.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:01.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.237][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:01.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:01.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:01.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:01.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:01.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:01.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:01.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:01.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:01.268][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:01.269][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:01.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:01.277][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:01.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:01.279][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:01.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:01.282][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:01.296][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:01.297][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:01.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:01.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:01.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:01.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:01.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:01.313][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:01.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:01.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:01.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:01.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:01.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:01.339][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:01.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:01.341][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.345][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.350][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:01.354][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:01.355][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:01.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:01.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:01.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:01.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:01.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:01.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.376][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:01.380][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:01.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:01.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:01.388][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:01.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:01.391][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:01.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:01.393][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.402][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:01.407][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:01.408][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:01.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:01.416][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:01.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:01.420][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:01.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:01.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.431][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:01.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:01.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:01.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:01.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:01.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:01.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:01.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:01.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:01.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:01.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:01.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:01.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:01.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:01.516][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:01.519][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:41:01.520][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:41:01.522][private$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[2025-03-21 19:41:01.875][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[2025-03-21 19:41:02.223][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:41:02.226][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-03-21 19:41:02.233][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-03-21 19:41:02.237][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[2025-03-21 19:41:02.242][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:41:02.243][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:41:02.247][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-21 19:41:02.599][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-21 19:41:02.953][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:41:02.956][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-03-21 19:41:02.962][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-03-21 19:41:02.967][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:02.981][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:02.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:02.988][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:02.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:02.990][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:02.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:02.993][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-03-21 19:41:02.994][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:41:02.996][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-03-21 19:41:02.998][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:41:02.999][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:41:03.000][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:41:03.001][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:41:03.002][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:41:03.004][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:41:03.007][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:03.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:03.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:03.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:03.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:03.019][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:03.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:03.021][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-03-21 19:41:03.024][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:41:03.025][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:41:03.027][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-03-21 19:41:03.396][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-03-21 19:41:03.761][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:41:03.764][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-03-21 19:41:03.767][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-03-21 19:41:03.770][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-03-21 19:41:03.772][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:41:03.773][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:41:03.775][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:41:03.777][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:03.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:03.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:03.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:03.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:03.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:03.790][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.TRACE[2025-03-21 19:41:03.792][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:03.794][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:03.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.795][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:03.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:03.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.800][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:41:03.801][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:41:03.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.803][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.804][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:41:03.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:41:03.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.809][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:41:03.810][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:41:03.811][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.813][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.815][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:41:03.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:41:03.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.819][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:41:03.820][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:41:03.821][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.822][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.823][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:41:03.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:41:03.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.828][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:41:03.829][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:41:03.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.831][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.833][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:41:03.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:41:03.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.838][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:03.839][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:03.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.842][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.843][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:03.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:03.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.846][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:41:03.847][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:03.848][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.849][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.850][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:41:03.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:03.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.855][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:03.856][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:03.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.858][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:03.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:03.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.863][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:41:03.864][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:41:03.866][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.867][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.868][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:41:03.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:41:03.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.873][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:41:03.874][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:41:03.876][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.877][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.879][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:41:03.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:41:03.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.884][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:41:03.885][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:41:03.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.887][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.889][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:41:03.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:41:03.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:03.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:03.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.899][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:03.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:03.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:03.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:03.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:03.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:03.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:03.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:03.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:03.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:03.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:03.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:03.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:03.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:03.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:03.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:03.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:03.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:03.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:03.940][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-03-21 19:41:03.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:03.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:03.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:03.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:03.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:03.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:03.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:03.956][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:03.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:03.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:03.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:03.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:03.966][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:03.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:03.968][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:03.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:03.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.973][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:03.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:03.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:03.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:03.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:03.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:03.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:03.982][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:03.983][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:03.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:03.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:03.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:03.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:03.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:03.997][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-03-21 19:41:03.999][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:41:04.001][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-03-21 19:41:04.003][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:41:04.005][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:41:04.006][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:41:04.008][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:41:04.009][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:41:04.010][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:41:04.013][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:04.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:04.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:04.022][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:04.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:04.024][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:04.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:04.026][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-03-21 19:41:04.028][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:41:04.029][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:41:04.031][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-03-21 19:41:04.390][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-03-21 19:41:04.745][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:41:04.748][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-03-21 19:41:04.753][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-03-21 19:41:04.757][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-03-21 19:41:04.759][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:41:04.761][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:41:04.762][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:41:04.764][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:04.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:04.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:04.774][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:04.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:04.776][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:04.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:04.780][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:04.782][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:04.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.785][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:04.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:04.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.792][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:41:04.793][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:41:04.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.795][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.797][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:41:04.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:41:04.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.803][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:41:04.804][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:41:04.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.807][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.808][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:41:04.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:41:04.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.814][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:41:04.815][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:41:04.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.818][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.819][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:41:04.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:41:04.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.824][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:41:04.825][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:41:04.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.828][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.829][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:41:04.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:41:04.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.835][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:04.836][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:04.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.838][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.840][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:41:04.841][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:04.842][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.843][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.844][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:41:04.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:04.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.849][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:04.850][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:04.851][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.853][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:04.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:04.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.866][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:41:04.876][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:41:04.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.879][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.881][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:41:04.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:41:04.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.886][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:41:04.887][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:41:04.888][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.890][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.891][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:41:04.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:41:04.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.896][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:41:04.897][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:41:04.898][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.899][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.901][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:41:04.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:41:04.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.906][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:04.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:04.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:04.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:04.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:04.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:04.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:04.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:04.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:04.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:04.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:04.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:04.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:04.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:04.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:04.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:04.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:04.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:04.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:04.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:04.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:04.958][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-03-21 19:41:04.960][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:04.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:04.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:04.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:04.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:04.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:04.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:04.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:04.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:04.999][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:05.004][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:41:05.005][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-21 19:41:05.007][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:41:05.009][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-21 19:41:05.013][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.022][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.025][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.028][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.058][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.061][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.077][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.087][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.088][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.097][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.099][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.123][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.129][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.138][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.169][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.170][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.179][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.208][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.210][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.270][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.272][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.287][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.304][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.307][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.324][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.325][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.337][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.374][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.396][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.397][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.405][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.436][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.438][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.455][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.467][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.470][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.475][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.483][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.484][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.495][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.498][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.507][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.512][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.520][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.522][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.541][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.553][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.574][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.575][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.583][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.595][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.605][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.617][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.631][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.645][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.647][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.655][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.689][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:05.694][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:41:05.696][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-21 19:41:05.697][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:41:05.699][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-21 19:41:05.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.719][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.738][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.747][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.749][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.777][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.785][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.787][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.863][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.864][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.874][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.896][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.921][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.943][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.944][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.952][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.954][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:05.965][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:05.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:05.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:05.969][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:05.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:05.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:05.978][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:05.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:05.996][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:05.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:05.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:06.017][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:06.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:06.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:06.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:06.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:06.032][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:06.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:06.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:06.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:06.048][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:06.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:06.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:06.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:06.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:06.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:06.059][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:06.073][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:06.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:06.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:06.083][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:06.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:06.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:06.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:06.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.097][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:06.102][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:06.103][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:06.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:06.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:06.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:06.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:06.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:06.116][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:06.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:06.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:06.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:06.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:06.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:06.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:06.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:06.145][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:06.159][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:06.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:06.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:06.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:06.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:06.170][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:06.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:06.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:06.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:06.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:06.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:06.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:06.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:06.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:06.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:06.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.210][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:06.214][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:06.215][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:06.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:06.222][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:06.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:06.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:06.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:06.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.236][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:06.241][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:06.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:06.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:06.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:06.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:06.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:06.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:06.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:06.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:06.269][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:06.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:06.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:06.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:06.278][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:06.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:06.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:06.295][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:06.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:06.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:06.303][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:06.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:06.306][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:06.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:06.309][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:06.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.351][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-21 19:41:06.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-21 19:41:06.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-21 19:41:06.366][biodb::testThat]
biodb.INFO [2025-03-21 19:41:06.368][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-03-21 19:41:06.369][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:41:06.370][biodb::testThat]
biodb.TRACE[2025-03-21 19:41:06.375][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-21 19:41:06.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-21 19:41:06.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:06.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:06.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:06.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:06.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.389][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:06.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:06.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:06.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:06.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:06.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:06.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:06.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:06.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:06.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:06.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:06.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:06.412][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:06.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:06.417][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:06.421][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:41:06.422][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:41:06.424][private$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[2025-03-21 19:41:06.777][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[2025-03-21 19:41:07.133][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:41:07.136][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-03-21 19:41:07.141][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-03-21 19:41:07.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:07.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:07.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:07.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:07.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:07.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:07.160][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[2025-03-21 19:41:07.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:07.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:07.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:07.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:07.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:07.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:07.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:07.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:07.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:07.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:07.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:07.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:07.178][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[2025-03-21 19:41:07.182][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:41:07.184][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:41:07.186][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-21 19:41:07.539][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-21 19:41:07.888][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:41:07.891][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-03-21 19:41:07.896][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-03-21 19:41:07.900][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:07.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:07.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:07.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:07.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:07.913][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:07.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:07.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:07.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:07.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:07.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:07.920][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:07.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:07.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:07.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:07.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:07.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:07.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:07.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:07.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:07.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:07.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:07.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:07.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:07.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:07.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:07.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:07.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:07.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:07.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:07.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:07.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:07.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:07.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:07.955][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:07.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:07.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:07.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:07.961][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-21 19:41:07.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:07.965][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:07.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:07.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:07.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:07.992][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:07.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:07.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:07.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:07.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.015][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:08.015][private$selectFields]
biodb.TRACE[2025-03-21 19:41:08.016][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-21 19:41:08.018][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-21 19:41:08.019][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:08.020][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.021][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.022][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.024][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.025][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.026][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.028][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.030][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:08.031][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:08.032][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.034][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.036][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.038][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-21 19:41:08.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.067][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-21 19:41:08.069][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:08.070][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:08.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:08.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:08.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:08.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:08.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:08.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.092][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:08.093][private$selectFields]
biodb.TRACE[2025-03-21 19:41:08.094][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-21 19:41:08.095][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-21 19:41:08.096][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:08.098][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.099][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.102][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.103][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.104][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.107][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.108][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:08.110][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:08.111][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.113][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.115][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.116][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-21 19:41:08.117][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.127][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.132][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-21 19:41:08.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:08.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:08.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:08.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:08.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:08.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:08.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:08.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.158][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:08.159][private$selectFields]
biodb.TRACE[2025-03-21 19:41:08.161][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-21 19:41:08.162][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-21 19:41:08.163][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:08.165][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.166][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.168][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.169][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.171][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.173][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.175][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:08.176][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:08.177][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.179][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.181][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.183][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-21 19:41:08.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:08.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.199][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-21 19:41:08.200][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-21 19:41:08.201][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-21 19:41:08.215][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:08.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:08.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:08.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:08.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:08.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:08.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:08.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:08.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:08.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:08.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:08.312][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:08.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:08.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:08.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:08.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:08.324][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:08.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:08.328][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:08.332][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:41:08.333][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:41:08.335][private$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[2025-03-21 19:41:08.688][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[2025-03-21 19:41:09.040][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:41:09.043][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-03-21 19:41:09.048][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-03-21 19:41:09.053][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[2025-03-21 19:41:09.057][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:41:09.073][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:41:09.075][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-21 19:41:09.427][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-21 19:41:09.778][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:41:09.780][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-03-21 19:41:09.785][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-03-21 19:41:09.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:09.789][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:09.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:09.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:09.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:09.797][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:09.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:09.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:09.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:09.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:09.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:09.803][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:09.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:09.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:09.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:09.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:09.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:09.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:09.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:09.811][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:09.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:09.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:09.818][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:09.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:09.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:09.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:09.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:09.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:09.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:09.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:09.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:09.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:09.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:09.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:09.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:09.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:09.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:09.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:09.835][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:09.836][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:09.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:09.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:09.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:09.845][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:09.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:09.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:09.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:09.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:09.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:09.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:09.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:09.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:09.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:09.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:09.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:09.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:09.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:09.889][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-21 19:41:09.911][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:09.912][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:09.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:09.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:09.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:09.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:09.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:09.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:09.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:09.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:09.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:09.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:09.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:09.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:09.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:09.931][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:09.932][private$selectFields]
biodb.TRACE[2025-03-21 19:41:09.932][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-21 19:41:09.933][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-21 19:41:09.934][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:09.936][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:09.937][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:09.938][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:09.939][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:09.940][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:09.941][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:09.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:09.943][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:09.944][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:09.945][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:09.946][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:09.947][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:09.949][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:09.949][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:09.950][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-21 19:41:09.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:09.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:09.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:09.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:09.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:09.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:09.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:09.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:09.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:09.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:09.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:09.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:09.965][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-21 19:41:09.966][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:09.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:09.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:09.974][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:09.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:09.976][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:09.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:09.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:09.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.004][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.047][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.048][private$selectFields]
biodb.TRACE[2025-03-21 19:41:10.050][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-21 19:41:10.051][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-21 19:41:10.052][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.054][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.055][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.058][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.059][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.060][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.061][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.062][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.063][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.077][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.078][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.079][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.082][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.083][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-21 19:41:10.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.090][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.101][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-21 19:41:10.102][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:10.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:10.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:10.112][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:10.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:10.114][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:10.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:10.117][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.127][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.128][private$selectFields]
biodb.TRACE[2025-03-21 19:41:10.129][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-21 19:41:10.131][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-21 19:41:10.131][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.132][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.133][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.135][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.136][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.137][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.139][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.140][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.141][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.143][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.144][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.146][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.147][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-21 19:41:10.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.162][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-21 19:41:10.163][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-21 19:41:10.164][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-21 19:41:10.174][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-21 19:41:10.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-21 19:41:10.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-21 19:41:10.183][biodb::testThat]
biodb.INFO [2025-03-21 19:41:10.184][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-03-21 19:41:10.186][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:41:10.187][biodb::testThat]
biodb.TRACE[2025-03-21 19:41:10.191][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-21 19:41:10.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-21 19:41:10.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.197][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.202][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.207][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:10.221][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:10.223][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:10.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:10.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:10.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:10.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:10.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:10.241][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:10.246][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:41:10.248][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-21 19:41:10.250][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:41:10.252][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-21 19:41:10.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:10.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:10.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:10.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:10.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:10.270][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:10.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:10.273][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:10.290][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:10.294][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:41:10.296][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-21 19:41:10.298][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:41:10.300][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-21 19:41:10.304][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:10.305][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:10.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:10.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:10.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:10.315][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:10.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:10.317][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.322][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:10.332][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:10.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:10.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:10.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:10.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:10.346][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:10.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:10.349][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:10.363][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-21 19:41:10.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:10.367][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:10.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:10.373][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:10.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:10.375][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:10.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:10.377][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.385][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.386][private$selectFields]
biodb.TRACE[2025-03-21 19:41:10.387][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-21 19:41:10.388][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-21 19:41:10.389][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.391][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.392][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.393][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.394][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.396][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.397][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.398][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.399][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.400][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.401][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.403][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.404][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.406][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.408][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-21 19:41:10.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.422][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-21 19:41:10.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:10.424][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:10.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:10.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:10.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:10.434][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:10.435][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[2025-03-21 19:41:10.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.444][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.444][private$selectFields]
biodb.TRACE[2025-03-21 19:41:10.445][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-21 19:41:10.446][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-21 19:41:10.447][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.448][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.449][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.451][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.452][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.453][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.455][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.456][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.457][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.457][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.458][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.459][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.460][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.462][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-21 19:41:10.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.482][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-21 19:41:10.483][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:10.484][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:10.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:10.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:10.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:10.492][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:10.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:10.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.502][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.503][private$selectFields]
biodb.TRACE[2025-03-21 19:41:10.504][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-21 19:41:10.505][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-21 19:41:10.506][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.507][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.508][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.511][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.512][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.513][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.514][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.515][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.516][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.517][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.518][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.521][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.522][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-21 19:41:10.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.534][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-21 19:41:10.535][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-21 19:41:10.535][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-21 19:41:10.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:10.563][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:10.564][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:10.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:10.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:10.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:10.572][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:10.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:10.575][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:10.579][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:41:10.580][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-21 19:41:10.581][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:41:10.582][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-21 19:41:10.585][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:10.588][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:41:10.589][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-21 19:41:10.590][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:41:10.592][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-21 19:41:10.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:10.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:10.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:10.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:10.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:10.604][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:10.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:10.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.613][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:10.616][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:10.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:10.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:10.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:10.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:10.627][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:10.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:10.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.634][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.638][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:10.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:10.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:10.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:10.650][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:10.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:10.652][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:10.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:10.655][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:10.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:10.669][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-21 19:41:10.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:10.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:10.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:10.680][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:10.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:10.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:10.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:10.685][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.689][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.694][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.695][private$selectFields]
biodb.TRACE[2025-03-21 19:41:10.696][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-21 19:41:10.697][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-21 19:41:10.698][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.700][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.701][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.702][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.703][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.704][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.705][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.706][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.707][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.708][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.709][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.710][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.712][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.713][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-21 19:41:10.714][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.727][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-21 19:41:10.728][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:10.729][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:10.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:10.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:10.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:10.737][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:10.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:10.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.745][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.748][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.749][private$selectFields]
biodb.TRACE[2025-03-21 19:41:10.750][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-21 19:41:10.751][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-21 19:41:10.752][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.753][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.754][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.756][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.757][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.758][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.760][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.762][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.764][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.765][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.766][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.768][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.771][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.772][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-21 19:41:10.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.789][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-21 19:41:10.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:10.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:10.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:10.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:10.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:10.804][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:10.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:10.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.815][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.816][private$selectFields]
biodb.TRACE[2025-03-21 19:41:10.817][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-21 19:41:10.818][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-21 19:41:10.819][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.821][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.822][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.824][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.825][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.825][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.828][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.829][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.831][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:10.832][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.833][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.834][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.835][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.837][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-21 19:41:10.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:10.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.851][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-21 19:41:10.852][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-21 19:41:10.853][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-21 19:41:10.865][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-21 19:41:10.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-21 19:41:10.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-21 19:41:10.885][biodb::testThat]
biodb.INFO [2025-03-21 19:41:10.886][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-03-21 19:41:10.887][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:41:10.888][biodb::testThat]
biodb.TRACE[2025-03-21 19:41:10.893][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-21 19:41:10.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-21 19:41:10.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.898][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.903][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.908][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:10.920][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:10.921][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:10.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:10.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:10.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:10.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:10.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:10.934][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:10.938][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:41:10.940][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-21 19:41:10.941][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:41:10.942][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-21 19:41:10.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:10.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:10.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:10.953][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:10.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:10.955][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:10.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:10.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:10.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:10.973][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:10.976][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:41:10.978][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-21 19:41:10.979][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:41:10.980][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-21 19:41:10.983][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:10.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:10.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:10.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:10.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:10.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:10.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:10.995][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:10.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:10.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.001][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:11.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:11.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.005][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:11.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:11.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:11.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:11.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:11.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:11.017][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:11.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:11.019][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:11.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:11.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:11.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:11.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:11.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:11.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.029][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:11.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:11.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:11.034][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-21 19:41:11.035][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:11.036][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:11.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:11.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:11.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:11.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:11.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:11.048][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.056][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.057][private$selectFields]
biodb.TRACE[2025-03-21 19:41:11.058][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-21 19:41:11.059][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-21 19:41:11.060][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.061][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.062][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.065][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.066][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.068][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.070][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.071][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.072][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.072][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.074][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.076][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.077][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-21 19:41:11.078][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.091][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-21 19:41:11.092][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:11.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:11.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:11.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:11.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:11.103][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:11.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:11.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.113][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.114][private$selectFields]
biodb.TRACE[2025-03-21 19:41:11.115][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-21 19:41:11.116][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-21 19:41:11.117][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.118][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.119][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.120][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.121][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.123][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.124][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.125][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.126][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.127][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.128][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.130][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.131][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-21 19:41:11.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.146][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-21 19:41:11.147][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:11.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:11.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:11.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:11.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:11.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:11.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:11.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.168][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.169][private$selectFields]
biodb.TRACE[2025-03-21 19:41:11.169][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-21 19:41:11.170][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-21 19:41:11.171][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.172][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.174][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.175][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.176][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.177][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.179][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.181][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.182][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.182][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.184][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.186][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.187][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-21 19:41:11.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.198][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-21 19:41:11.199][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-21 19:41:11.200][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-21 19:41:11.224][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.231][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:11.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:11.245][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:11.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:11.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:11.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:11.255][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:11.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:11.258][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:11.262][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:41:11.263][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-21 19:41:11.264][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:41:11.265][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-21 19:41:11.268][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:11.271][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:41:11.273][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-21 19:41:11.274][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:41:11.275][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-21 19:41:11.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:11.283][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:11.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:11.290][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:11.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:11.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:11.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:11.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:11.307][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:11.308][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:11.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:11.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:11.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:11.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:11.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:11.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:11.331][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:11.332][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:11.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:11.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:11.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:11.342][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:11.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:11.345][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.354][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:11.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:11.359][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-21 19:41:11.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:11.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:11.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:11.370][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:11.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:11.371][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:11.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:11.374][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.381][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.382][private$selectFields]
biodb.TRACE[2025-03-21 19:41:11.383][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-21 19:41:11.384][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-21 19:41:11.385][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.385][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.386][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.388][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.389][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.390][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.391][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.392][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.393][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.394][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.395][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.396][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.397][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.398][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-21 19:41:11.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.414][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-21 19:41:11.415][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:11.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:11.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:11.424][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:11.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:11.426][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:11.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:11.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.435][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.436][private$selectFields]
biodb.TRACE[2025-03-21 19:41:11.437][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-21 19:41:11.438][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-21 19:41:11.439][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.440][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.441][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.442][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.443][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.444][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.446][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.447][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.448][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.449][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.450][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.451][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.452][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-21 19:41:11.453][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.465][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-21 19:41:11.466][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:11.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:11.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:11.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:11.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:11.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:11.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:11.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.487][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.488][private$selectFields]
biodb.TRACE[2025-03-21 19:41:11.489][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-21 19:41:11.490][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-21 19:41:11.491][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.492][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.493][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.495][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.496][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.497][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.497][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.498][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.499][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.501][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-21 19:41:11.502][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.503][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.505][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.505][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-21 19:41:11.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:11.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:11.522][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-21 19:41:11.523][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-21 19:41:11.525][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-21 19:41:11.572][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-21 19:41:11.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-21 19:41:11.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:11.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-21 19:41:11.582][biodb::testThat]
biodb.INFO [2025-03-21 19:41:11.583][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-03-21 19:41:11.584][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:41:11.585][biodb::testThat]
biodb.DEBUG[2025-03-21 19:41:11.587][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-03-21 19:41:11.589][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:41:11.591][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-03-21 19:41:11.592][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:41:11.593][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:41:11.594][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:41:11.595][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:41:11.596][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:41:11.597][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:41:11.600][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:11.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:11.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:11.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:11.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:11.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:11.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:11.615][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-03-21 19:41:11.618][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:41:11.618][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:41:11.620][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-03-21 19:41:12.035][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-03-21 19:41:12.394][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:41:12.397][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-03-21 19:41:12.400][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-03-21 19:41:12.403][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-03-21 19:41:12.406][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:41:12.407][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:41:12.408][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:41:12.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:12.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:12.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:12.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:12.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:12.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:12.422][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[2025-03-21 19:41:12.424][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:12.426][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:12.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.428][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:12.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:12.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:12.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:12.434][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:41:12.435][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:41:12.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.438][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:12.439][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:41:12.441][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:41:12.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.443][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:12.445][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:41:12.446][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:41:12.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.449][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:12.450][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:41:12.451][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:41:12.452][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.453][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:12.454][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:12.455][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:12.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.470][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:12.471][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:41:12.473][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:12.474][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.476][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:12.477][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:12.479][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:12.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.481][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:12.482][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:41:12.483][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:41:12.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.485][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:12.486][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:41:12.498][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:41:12.500][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.501][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:12.503][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:41:12.504][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:41:12.505][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.507][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:12.508][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:12.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:12.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:12.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:12.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:12.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:12.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:12.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:12.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:12.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:12.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:12.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:12.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:12.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:12.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:12.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:12.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:12.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:12.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:12.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:12.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:12.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:12.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:12.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:12.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:12.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:12.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:12.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:12.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:12.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:12.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:12.553][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-03-21 19:41:12.554][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-03-21 19:41:12.564][biodb::testThat]
biodb.INFO [2025-03-21 19:41:12.566][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-03-21 19:41:12.567][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:41:12.567][biodb::testThat]
biodb.DEBUG[2025-03-21 19:41:12.577][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-03-21 19:41:12.578][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-03-21 19:41:12.579][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-03-21 19:41:12.580][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-03-21 19:41:12.582][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-03-21 19:41:12.583][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:41:12.585][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:41:12.586][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:41:12.587][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:41:12.588][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:41:12.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:12.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:12.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:12.600][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:12.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:12.602][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:12.604][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[2025-03-21 19:41:12.605][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-03-21 19:41:12.608][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:41:12.610][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:41:12.612][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-03-21 19:41:12.970][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-03-21 19:41:13.325][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:41:13.327][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-03-21 19:41:13.332][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-03-21 19:41:13.334][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:13.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:13.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:13.344][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:13.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:13.346][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:13.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:13.349][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-03-21 19:41:13.352][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:41:13.353][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:41:13.354][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-03-21 19:41:13.716][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-03-21 19:41:14.071][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:41:14.076][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-03-21 19:41:14.081][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-03-21 19:41:14.083][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:14.094][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:14.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:14.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:14.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:14.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:14.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:14.148][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-03-21 19:41:14.151][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:41:14.152][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:41:14.154][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-03-21 19:41:14.517][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-03-21 19:41:14.878][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:41:14.881][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-03-21 19:41:14.885][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-03-21 19:41:14.889][private$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[2025-03-21 19:41:14.892][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:41:14.894][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-03-21 19:41:14.895][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-03-21 19:41:14.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:14.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:14.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:14.905][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:14.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:14.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:14.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:14.910][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:14.911][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:14.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:14.912][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:14.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:14.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:14.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:14.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:14.919][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:41:14.920][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:41:14.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:14.922][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:14.923][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:41:14.924][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:41:14.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:14.927][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:14.928][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:41:14.929][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:41:14.930][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:14.931][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:14.932][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:41:14.933][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:41:14.934][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:14.935][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:14.937][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:14.938][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:14.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:14.940][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:14.942][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:41:14.943][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:14.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:14.945][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:14.947][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:14.948][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:14.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:14.950][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:14.952][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:41:14.953][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:41:14.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:14.956][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:14.958][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:41:14.959][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:41:14.960][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:14.961][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:14.962][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:41:14.964][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:41:14.965][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:14.965][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:14.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:14.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:14.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:14.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:14.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:14.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:14.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:14.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:14.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:14.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:14.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:14.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:14.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:14.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:14.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:14.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:14.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:14.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:14.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:14.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:14.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:14.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:14.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:14.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:14.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:14.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:14.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:14.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:14.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:14.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:14.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:15.005][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:15.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:15.007][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:15.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:15.010][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:15.011][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:15.012][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.013][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:15.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:15.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.018][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:41:15.019][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:41:15.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.021][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.023][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:41:15.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:41:15.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.029][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:41:15.030][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:41:15.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.033][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.035][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:41:15.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:41:15.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.041][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:41:15.042][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:41:15.043][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.045][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.046][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:41:15.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:41:15.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.052][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:41:15.053][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:41:15.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.056][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.058][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:41:15.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:41:15.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.063][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:15.064][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:15.065][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.066][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.067][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:15.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:15.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.072][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:41:15.073][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:15.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.075][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.076][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:41:15.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:15.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.082][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:15.083][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:15.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.086][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.087][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:15.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:15.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.093][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:41:15.094][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:41:15.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.097][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.098][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:41:15.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:41:15.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.103][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:41:15.105][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:41:15.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.107][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.109][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:41:15.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:41:15.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.113][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:41:15.115][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:41:15.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.117][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.136][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:41:15.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:41:15.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:15.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:15.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.146][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:15.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:15.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:15.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:15.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:15.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:15.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:15.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:15.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:15.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:15.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:15.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:15.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:15.175][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:15.176][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:15.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:15.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:15.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:15.186][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:15.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:15.191][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:15.193][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:15.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.195][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:15.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:15.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.201][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:41:15.203][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:41:15.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.204][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.206][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:41:15.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:41:15.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.210][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:41:15.211][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:41:15.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.213][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.214][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:41:15.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:41:15.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.218][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:41:15.220][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:41:15.221][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.222][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.223][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:41:15.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:41:15.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.227][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:41:15.228][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:41:15.229][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.230][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.231][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:41:15.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:41:15.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.237][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:15.238][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:15.239][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.240][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.242][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:15.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:15.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.247][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:41:15.248][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:15.250][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.251][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.253][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:41:15.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:15.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.258][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:15.259][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:15.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.261][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:15.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:15.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.266][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:41:15.267][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:41:15.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.270][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.272][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:41:15.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:41:15.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.276][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:41:15.278][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:41:15.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.280][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.281][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:41:15.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:41:15.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.287][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:41:15.289][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:41:15.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.291][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.292][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:41:15.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:41:15.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:15.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:15.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:15.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:15.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:15.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:15.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:15.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:15.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:15.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:15.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:15.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:15.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:15.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:15.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:15.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:15.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:15.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:15.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:15.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:15.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:15.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:15.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:15.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:15.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:15.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:15.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:15.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:15.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:15.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:15.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:15.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:15.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:15.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:15.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:15.372][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-03-21 19:41:15.373][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-03-21 19:41:15.374][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-03-21 19:41:15.392][biodb::testThat]
biodb.INFO [2025-03-21 19:41:15.394][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-03-21 19:41:15.395][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:41:15.396][biodb::testThat]
biodb.INFO [2025-03-21 19:41:15.425][biodb::testThat]
biodb.INFO [2025-03-21 19:41:15.427][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-03-21 19:41:15.428][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:41:15.429][biodb::testThat]
biodb.INFO [2025-03-21 19:41:15.440][biodb::testThat]
biodb.INFO [2025-03-21 19:41:15.442][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-03-21 19:41:15.443][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:41:15.444][biodb::testThat]
biodb.DEBUG[2025-03-21 19:41:15.446][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:15.451][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:41:15.451][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:41:15.453][private$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[2025-03-21 19:41:15.893][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[2025-03-21 19:41:16.388][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:41:16.390][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-03-21 19:41:16.394][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-03-21 19:41:16.408][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:41:16.410][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:41:16.411][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:16.412][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:16.413][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:16.414][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:16.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:16.416][ef$get] fields variable is a list.
biodb.INFO [2025-03-21 19:41:16.418][biodb::testThat]
biodb.INFO [2025-03-21 19:41:16.419][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2025-03-21 19:41:16.421][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:41:16.421][biodb::testThat]
biodb.ERROR[2025-03-21 19:41:16.438][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-03-21 19:41:16.461][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-03-21 19:41:16.479][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-21 19:41:16.481][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-21 19:41:16.483][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-21 19:41:16.484][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-21 19:41:16.485][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:16.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:16.488][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.490][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-21 19:41:16.513][biodb::testContext]
biodb.INFO [2025-03-21 19:41:16.514][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-21 19:41:16.515][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-03-21 19:41:16.516][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-21 19:41:16.517][biodb::testContext]
biodb.INFO [2025-03-21 19:41:16.518][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-21 19:41:16.520][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-21 19:41:16.524][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-21 19:41:16.525][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-21 19:41:16.526][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-21 19:41:16.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.529][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-21 19:41:16.530][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-21 19:41:16.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.535][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-21 19:41:16.536][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-21 19:41:16.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.540][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-21 19:41:16.541][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-21 19:41:16.542][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-21 19:41:16.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.546][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-21 19:41:16.548][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-21 19:41:16.549][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-21 19:41:16.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.552][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-21 19:41:16.553][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-21 19:41:16.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.556][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[2025-03-21 19:41:16.557][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-21 19:41:16.558][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-21 19:41:16.559][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-21 19:41:16.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.562][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-21 19:41:16.563][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-21 19:41:16.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.565][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[2025-03-21 19:41:16.566][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-21 19:41:16.567][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-21 19:41:16.568][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-21 19:41:16.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.572][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-21 19:41:16.573][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-21 19:41:16.574][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-21 19:41:16.575][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-21 19:41:16.576][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-21 19:41:16.577][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-21 19:41:16.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.579][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[2025-03-21 19:41:16.580][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-21 19:41:16.581][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-21 19:41:16.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.584][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-21 19:41:16.585][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-21 19:41:16.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.589][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-21 19:41:16.590][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-21 19:41:16.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.595][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-21 19:41:16.596][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-21 19:41:16.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.599][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[2025-03-21 19:41:16.601][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-21 19:41:16.601][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-21 19:41:16.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.605][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-21 19:41:16.606][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-21 19:41:16.627][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-21 19:41:16.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.631][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-21 19:41:16.633][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-21 19:41:16.634][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-21 19:41:16.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.638][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-21 19:41:16.640][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:16.642][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-21 19:41:16.643][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:16.644][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-21 19:41:16.645][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:16.646][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-21 19:41:16.647][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:16.648][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-21 19:41:16.649][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-21 19:41:16.650][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-21 19:41:16.651][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:16.652][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-21 19:41:16.653][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-21 19:41:16.654][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:16.655][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:16.656][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-21 19:41:16.656][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-21 19:41:16.656][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-21 19:41:16.656][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-21 19:41:16.656][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-21 19:41:16.657][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-21 19:41:16.658][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:16.659][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:16.660][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-21 19:41:16.661][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:16.662][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:16.664][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-21 19:41:16.665][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:16.666][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-21 19:41:16.667][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-21 19:41:16.668][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:16.669][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:16.670][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-21 19:41:16.672][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:16.673][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-21 19:41:16.674][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:16.676][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-21 19:41:16.677][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:16.678][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-21 19:41:16.680][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:16.681][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-21 19:41:16.682][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-21 19:41:16.683][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-21 19:41:16.684][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:16.685][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-21 19:41:16.686][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-21 19:41:16.687][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:16.687][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:16.689][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-21 19:41:16.689][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-21 19:41:16.689][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-21 19:41:16.689][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-21 19:41:16.689][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-21 19:41:16.690][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-21 19:41:16.691][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:16.692][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:16.693][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-21 19:41:16.693][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:16.694][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:16.695][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-21 19:41:16.696][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:16.697][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-21 19:41:16.698][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-21 19:41:16.699][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:16.701][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:16.702][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-21 19:41:16.703][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:16.704][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-21 19:41:16.705][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:16.706][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-21 19:41:16.708][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:16.709][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-21 19:41:16.710][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:16.711][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-21 19:41:16.712][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-21 19:41:16.712][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-21 19:41:16.713][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:16.714][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-21 19:41:16.715][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-21 19:41:16.716][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:16.717][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:16.718][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:16.720][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-21 19:41:16.721][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:16.722][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:16.724][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-21 19:41:16.725][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:16.726][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:16.727][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-21 19:41:16.728][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:16.729][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-21 19:41:16.729][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-21 19:41:16.730][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:16.731][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:16.732][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-21 19:41:16.734][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:16.735][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-21 19:41:16.735][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:16.736][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-21 19:41:16.737][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:16.738][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-21 19:41:16.739][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:16.740][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-21 19:41:16.740][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-21 19:41:16.741][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-21 19:41:16.742][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:16.743][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-21 19:41:16.744][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-21 19:41:16.745][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:16.746][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:16.746][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:16.747][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-21 19:41:16.748][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:16.749][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:16.751][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-21 19:41:16.752][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:16.753][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:16.755][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-21 19:41:16.756][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:16.757][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-21 19:41:16.758][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-21 19:41:16.759][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:16.760][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:16.761][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-21 19:41:16.762][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.763][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[2025-03-21 19:41:16.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.791][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[2025-03-21 19:41:16.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.802][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[2025-03-21 19:41:16.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.806][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[2025-03-21 19:41:16.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.812][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[2025-03-21 19:41:16.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.817][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[2025-03-21 19:41:16.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.838][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-21 19:41:16.840][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-21 19:41:16.841][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-21 19:41:16.843][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-21 19:41:16.844][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-21 19:41:16.845][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-21 19:41:16.847][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-21 19:41:16.848][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-21 19:41:16.850][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-21 19:41:16.852][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-21 19:41:16.854][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-21 19:41:16.855][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-21 19:41:16.857][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-21 19:41:16.858][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-21 19:41:16.860][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-21 19:41:16.862][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-21 19:41:16.864][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-21 19:41:16.865][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-21 19:41:16.867][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-21 19:41:16.868][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-21 19:41:16.869][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-21 19:41:16.871][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-21 19:41:16.879][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-21 19:41:16.880][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-21 19:41:16.881][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-21 19:41:16.883][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-21 19:41:16.884][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-21 19:41:16.885][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-21 19:41:16.887][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-21 19:41:16.888][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-21 19:41:16.890][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-21 19:41:16.891][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-21 19:41:16.892][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-21 19:41:16.894][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-21 19:41:16.896][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-21 19:41:16.898][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-21 19:41:16.899][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-21 19:41:16.900][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-21 19:41:16.902][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-21 19:41:16.903][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-21 19:41:16.904][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-21 19:41:16.905][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-21 19:41:16.907][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-21 19:41:16.908][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-21 19:41:16.909][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-21 19:41:16.911][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-21 19:41:16.912][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-21 19:41:16.913][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-21 19:41:16.915][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-21 19:41:16.916][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-21 19:41:16.917][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-21 19:41:16.919][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-21 19:41:16.920][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-21 19:41:16.921][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-21 19:41:16.923][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-21 19:41:16.924][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-21 19:41:16.925][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-21 19:41:16.926][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-21 19:41:16.928][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-21 19:41:16.929][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-21 19:41:16.930][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-21 19:41:16.932][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-21 19:41:16.933][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-21 19:41:16.934][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-21 19:41:16.936][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-21 19:41:16.937][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-21 19:41:16.939][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-21 19:41:16.940][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-21 19:41:16.941][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-21 19:41:16.943][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-21 19:41:16.944][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-21 19:41:16.946][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-21 19:41:16.947][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-21 19:41:16.948][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-21 19:41:16.949][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-21 19:41:16.950][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-21 19:41:16.951][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-21 19:41:16.952][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-21 19:41:16.953][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-21 19:41:16.955][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-21 19:41:16.956][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-21 19:41:16.958][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-21 19:41:16.959][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-21 19:41:16.961][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-21 19:41:16.963][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-21 19:41:16.965][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-21 19:41:16.966][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.967][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:16.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:16.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:16.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:16.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:16.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:16.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:16.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:16.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.991][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[2025-03-21 19:41:16.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:16.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:16.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:16.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:16.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:16.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:16.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:16.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:16.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:17.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:17.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:17.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:17.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:17.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:17.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:17.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:17.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:17.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:17.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:17.009][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[2025-03-21 19:41:17.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:17.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:17.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:17.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:17.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:17.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:17.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:17.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:17.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:17.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:17.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:17.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:17.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:17.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:17.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:17.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:17.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:17.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:17.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:17.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:17.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:17.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:17.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:17.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:17.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:17.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:17.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:17.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:17.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:17.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:17.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:17.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:17.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:17.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:17.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:17.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:17.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:17.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:17.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:17.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:17.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:17.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:17.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:17.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:17.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:17.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:17.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:17.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:17.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:17.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:17.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:17.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:17.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:17.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:17.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:17.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:17.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:17.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:17.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:17.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:17.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:17.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:17.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:17.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:17.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:17.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:17.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:17.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:17.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:17.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:17.075][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-21 19:41:17.077][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-21 19:41:17.078][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:17.080][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-21 19:41:17.080][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:17.081][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-21 19:41:17.082][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:17.083][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-21 19:41:17.084][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:17.085][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-21 19:41:17.086][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-21 19:41:17.087][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-21 19:41:17.088][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:17.089][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-21 19:41:17.090][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-21 19:41:17.091][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-21 19:41:17.091][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-21 19:41:17.091][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-21 19:41:17.091][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-21 19:41:17.091][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-21 19:41:17.091][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-21 19:41:17.091][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-21 19:41:17.091][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-21 19:41:17.091][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-21 19:41:17.091][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-21 19:41:17.091][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-21 19:41:17.092][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:17.093][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-21 19:41:17.093][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-21 19:41:17.093][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-21 19:41:17.095][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-21 19:41:17.096][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:17.097][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:17.098][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-21 19:41:17.099][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:17.100][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:17.101][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-21 19:41:17.102][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:41:17.102][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-21 19:41:17.103][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-21 19:41:17.105][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-21 19:41:17.106][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:17.107][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-21 19:41:17.107][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-21 19:41:17.109][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-21 19:41:17.111][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-21 19:41:17.113][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-21 19:41:17.115][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-21 19:41:17.117][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-21 19:41:17.119][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-21 19:41:17.123][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-21 19:41:17.125][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-21 19:41:17.126][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-21 19:41:17.129][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-21 19:41:17.130][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-21 19:41:17.131][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-21 19:41:17.133][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-21 19:41:17.134][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-21 19:41:17.135][biodb::testThat]
biodb.INFO [2025-03-21 19:41:17.137][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2025-03-21 19:41:17.138][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:41:17.139][biodb::testThat]
biodb.DEBUG[2025-03-21 19:41:17.144][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-21 19:41:17.148][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:41:17.150][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:41:17.151][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-03-21 19:41:17.486][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-03-21 19:41:18.035][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:41:18.038][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-03-21 19:41:18.043][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-03-21 19:41:18.049][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:18.054][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:41:18.055][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:41:18.058][private$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[2025-03-21 19:41:18.416][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[2025-03-21 19:41:18.770][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:41:18.774][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-03-21 19:41:18.779][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-03-21 19:41:18.782][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:18.784][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:18.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:18.793][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:18.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:18.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:18.798][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[2025-03-21 19:41:18.800][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[2025-03-21 19:41:18.805][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:41:18.807][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:41:18.809][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-21 19:41:19.160][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-21 19:41:19.511][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:41:19.515][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-03-21 19:41:19.522][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-03-21 19:41:19.526][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:19.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:19.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:19.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:19.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:19.543][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:19.544][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.DEBUG[2025-03-21 19:41:19.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:19.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:19.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:19.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:19.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:19.656][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:19.658][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[2025-03-21 19:41:19.680][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:19.687][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:41:19.690][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-21 19:41:19.692][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:41:19.694][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-21 19:41:19.706][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:19.708][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:19.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:19.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:19.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:19.725][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:19.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:19.736][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:19.741][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:41:19.744][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-21 19:41:19.746][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:41:19.758][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-21 19:41:19.761][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:19.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:19.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:19.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:19.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:19.778][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:19.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:19.781][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:19.788][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:19.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:19.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:19.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:19.805][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:19.807][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[2025-03-21 19:41:19.822][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:19.826][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:41:19.829][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-21 19:41:19.841][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:41:19.843][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-21 19:41:19.845][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:19.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:19.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:19.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:19.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:19.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:19.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:19.874][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:19.889][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:41:19.891][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-21 19:41:19.894][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:41:19.904][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-21 19:41:19.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:19.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:19.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:19.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:19.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:19.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:19.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:19.937][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:19.943][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:41:19.944][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:41:19.953][private$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[2025-03-21 19:41:20.308][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[2025-03-21 19:41:20.662][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:41:20.665][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-03-21 19:41:20.672][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-03-21 19:41:20.675][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:20.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:20.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:20.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:20.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:20.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:20.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-21 19:41:20.703][biodb::testThat]
biodb.INFO [2025-03-21 19:41:20.705][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2025-03-21 19:41:20.707][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:41:20.708][biodb::testThat]
biodb.DEBUG[2025-03-21 19:41:20.714][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[2025-03-21 19:41:20.719][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:41:20.721][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:41:20.725][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-21 19:41:21.080][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-21 19:41:21.433][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:41:21.436][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-03-21 19:41:21.442][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-03-21 19:41:21.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:21.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:21.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:21.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:21.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:21.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:21.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:21.466][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:21.470][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:41:21.472][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:41:21.475][private$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[2025-03-21 19:41:21.831][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[2025-03-21 19:41:22.186][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:41:22.189][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-03-21 19:41:22.195][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-03-21 19:41:22.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:22.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:22.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:22.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:22.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:22.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-21 19:41:22.221][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-21 19:41:22.223][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-21 19:41:22.225][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-21 19:41:22.226][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-21 19:41:22.228][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:22.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:22.231][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:22.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:22.233][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-21 19:41:22.240][biodb::testContext]
biodb.INFO [2025-03-21 19:41:22.242][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-21 19:41:22.244][biodb::testContext] Test context - Test web services
biodb.INFO [2025-03-21 19:41:22.245][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-21 19:41:22.246][biodb::testContext]
biodb.INFO [2025-03-21 19:41:22.250][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-21 19:41:22.252][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-21 19:41:22.259][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-21 19:41:22.260][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-21 19:41:22.262][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-21 19:41:22.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.268][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-21 19:41:22.269][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-21 19:41:22.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.275][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-21 19:41:22.276][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-21 19:41:22.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.281][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-21 19:41:22.283][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-21 19:41:22.284][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-21 19:41:22.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.290][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-21 19:41:22.291][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-21 19:41:22.293][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-21 19:41:22.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.298][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-21 19:41:22.299][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-21 19:41:22.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.305][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-21 19:41:22.306][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-21 19:41:22.308][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-21 19:41:22.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.313][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-21 19:41:22.315][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-21 19:41:22.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.318][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[2025-03-21 19:41:22.319][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-21 19:41:22.321][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-21 19:41:22.322][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-21 19:41:22.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.327][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-21 19:41:22.328][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-21 19:41:22.330][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-21 19:41:22.331][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-21 19:41:22.333][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-21 19:41:22.334][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-21 19:41:22.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.338][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[2025-03-21 19:41:22.339][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-21 19:41:22.340][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-21 19:41:22.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.345][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-21 19:41:22.346][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-21 19:41:22.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.351][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-21 19:41:22.353][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-21 19:41:22.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.357][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-21 19:41:22.359][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-21 19:41:22.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.364][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-21 19:41:22.365][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-21 19:41:22.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.371][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-21 19:41:22.372][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-21 19:41:22.407][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-21 19:41:22.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.411][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[2025-03-21 19:41:22.412][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-21 19:41:22.413][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-21 19:41:22.415][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-21 19:41:22.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.420][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-21 19:41:22.423][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:22.424][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-21 19:41:22.425][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:22.427][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-21 19:41:22.428][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:22.429][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-21 19:41:22.430][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:22.432][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-21 19:41:22.433][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-21 19:41:22.434][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-21 19:41:22.435][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:22.436][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-21 19:41:22.437][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-21 19:41:22.438][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:22.440][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:22.441][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-21 19:41:22.441][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-21 19:41:22.441][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-21 19:41:22.441][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-21 19:41:22.441][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-21 19:41:22.442][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-21 19:41:22.444][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:22.445][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:22.463][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-21 19:41:22.480][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:22.482][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:22.483][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-21 19:41:22.489][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:22.491][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-21 19:41:22.492][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-21 19:41:22.494][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:22.495][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:22.497][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-21 19:41:22.504][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:22.505][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-21 19:41:22.507][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:22.508][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-21 19:41:22.510][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:22.511][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-21 19:41:22.512][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:22.521][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-21 19:41:22.523][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-21 19:41:22.524][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-21 19:41:22.526][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:22.527][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-21 19:41:22.528][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-21 19:41:22.529][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:22.538][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:22.540][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-21 19:41:22.540][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-21 19:41:22.540][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-21 19:41:22.540][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-21 19:41:22.540][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-21 19:41:22.542][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-21 19:41:22.543][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:22.544][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:22.546][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-21 19:41:22.554][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:22.556][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:22.558][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-21 19:41:22.559][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:22.561][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-21 19:41:22.562][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-21 19:41:22.564][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:22.571][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:22.573][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-21 19:41:22.577][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:22.579][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-21 19:41:22.580][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:22.588][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-21 19:41:22.590][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:22.592][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-21 19:41:22.593][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:22.595][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-21 19:41:22.596][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-21 19:41:22.606][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-21 19:41:22.609][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:22.610][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-21 19:41:22.612][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-21 19:41:22.614][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:22.615][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:22.623][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:22.625][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-21 19:41:22.627][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:22.628][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:22.630][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-21 19:41:22.639][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:22.641][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:22.643][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-21 19:41:22.644][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:22.646][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-21 19:41:22.647][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-21 19:41:22.655][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:22.657][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:22.659][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-21 19:41:22.662][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:22.670][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-21 19:41:22.673][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:22.674][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-21 19:41:22.676][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:22.678][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-21 19:41:22.680][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:22.687][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-21 19:41:22.689][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-21 19:41:22.692][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-21 19:41:22.693][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:22.695][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-21 19:41:22.705][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-21 19:41:22.707][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:22.710][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:22.712][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:22.713][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-21 19:41:22.722][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:22.723][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:22.725][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-21 19:41:22.727][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:22.728][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:22.730][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-21 19:41:22.738][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:22.740][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-21 19:41:22.741][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-21 19:41:22.743][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:22.744][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:22.754][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-21 19:41:22.756][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.757][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[2025-03-21 19:41:22.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:22.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:22.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:22.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:22.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:22.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:22.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:22.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:22.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.805][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[2025-03-21 19:41:22.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:22.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:22.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.812][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[2025-03-21 19:41:22.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:22.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:22.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:22.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:22.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:22.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:22.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.852][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[2025-03-21 19:41:22.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:22.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:22.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.865][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[2025-03-21 19:41:22.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:22.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:22.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.873][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[2025-03-21 19:41:22.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:22.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:22.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:22.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:22.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:22.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:22.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:22.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:22.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:22.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:22.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:22.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:22.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.959][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[2025-03-21 19:41:22.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:22.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:22.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:22.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:22.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:22.994][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-21 19:41:22.998][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-21 19:41:23.000][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-21 19:41:23.009][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-21 19:41:23.013][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-21 19:41:23.016][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-21 19:41:23.019][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-21 19:41:23.026][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-21 19:41:23.029][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-21 19:41:23.032][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-21 19:41:23.041][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-21 19:41:23.044][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-21 19:41:23.046][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-21 19:41:23.049][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-21 19:41:23.055][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-21 19:41:23.058][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-21 19:41:23.061][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-21 19:41:23.071][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-21 19:41:23.075][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-21 19:41:23.079][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-21 19:41:23.087][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-21 19:41:23.090][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-21 19:41:23.094][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-21 19:41:23.105][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-21 19:41:23.108][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-21 19:41:23.111][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-21 19:41:23.121][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-21 19:41:23.124][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-21 19:41:23.127][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-21 19:41:23.137][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-21 19:41:23.140][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-21 19:41:23.144][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-21 19:41:23.156][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-21 19:41:23.160][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-21 19:41:23.163][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-21 19:41:23.172][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-21 19:41:23.175][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-21 19:41:23.185][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-21 19:41:23.187][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-21 19:41:23.190][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-21 19:41:23.192][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-21 19:41:23.202][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-21 19:41:23.205][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-21 19:41:23.208][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-21 19:41:23.210][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-21 19:41:23.212][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-21 19:41:23.219][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-21 19:41:23.222][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-21 19:41:23.224][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-21 19:41:23.226][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-21 19:41:23.237][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-21 19:41:23.240][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-21 19:41:23.242][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-21 19:41:23.244][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-21 19:41:23.251][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-21 19:41:23.254][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-21 19:41:23.256][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-21 19:41:23.258][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-21 19:41:23.260][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-21 19:41:23.270][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-21 19:41:23.273][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-21 19:41:23.275][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-21 19:41:23.278][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-21 19:41:23.287][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-21 19:41:23.290][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-21 19:41:23.292][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-21 19:41:23.294][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-21 19:41:23.302][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-21 19:41:23.304][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-21 19:41:23.307][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-21 19:41:23.309][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-21 19:41:23.319][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-21 19:41:23.321][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-21 19:41:23.323][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-21 19:41:23.325][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-21 19:41:23.332][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-21 19:41:23.334][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-21 19:41:23.337][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-21 19:41:23.339][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-21 19:41:23.341][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-21 19:41:23.350][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-21 19:41:23.352][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-21 19:41:23.355][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-21 19:41:23.364][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-21 19:41:23.367][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-21 19:41:23.370][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-21 19:41:23.371][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:23.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:23.374][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:23.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:23.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:23.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:23.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:23.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:23.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:23.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:23.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:23.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:23.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:23.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:23.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:23.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:23.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:23.422][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.DEBUG[2025-03-21 19:41:23.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:23.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:23.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:23.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:23.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:23.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:23.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:23.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:23.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:23.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:23.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:23.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:23.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:23.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:23.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:23.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:23.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:23.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:23.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:23.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:23.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:23.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:23.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:23.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:23.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:23.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:23.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:23.503][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[2025-03-21 19:41:23.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:23.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:23.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:23.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:23.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:23.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:23.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:23.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:23.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:23.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:23.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:23.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:23.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:23.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:23.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:23.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:23.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:23.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:23.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:23.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:23.551][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[2025-03-21 19:41:23.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:23.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:23.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:23.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:23.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:23.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:23.567][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[2025-03-21 19:41:23.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:23.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:23.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:23.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:23.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:23.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:23.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:23.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:23.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:23.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:23.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:23.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:23.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:23.601][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[2025-03-21 19:41:23.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:23.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:23.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:23.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:23.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:23.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:23.622][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[2025-03-21 19:41:23.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:23.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:23.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:23.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:23.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:23.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:23.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:23.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:23.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:23.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:23.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:23.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:23.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:23.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:23.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:23.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:23.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:23.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:23.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:23.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:23.661][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[2025-03-21 19:41:23.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:23.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:23.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:23.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:23.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:23.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:23.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:23.687][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-21 19:41:23.703][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-21 19:41:23.706][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:23.707][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-21 19:41:23.709][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:23.711][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-21 19:41:23.719][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:23.721][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-21 19:41:23.722][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:23.724][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-21 19:41:23.726][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-21 19:41:23.728][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-21 19:41:23.731][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:23.732][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-21 19:41:23.734][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-21 19:41:23.736][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-21 19:41:23.736][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-21 19:41:23.736][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-21 19:41:23.736][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-21 19:41:23.736][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-21 19:41:23.736][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-21 19:41:23.736][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-21 19:41:23.736][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-21 19:41:23.736][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-21 19:41:23.736][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-21 19:41:23.736][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-21 19:41:23.738][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:23.739][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-21 19:41:23.739][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-21 19:41:23.739][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-21 19:41:23.747][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-21 19:41:23.748][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:23.750][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:23.751][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-21 19:41:23.753][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:23.754][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:23.760][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-21 19:41:23.762][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:41:23.762][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-21 19:41:23.764][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-21 19:41:23.766][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-21 19:41:23.767][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:23.769][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-21 19:41:23.769][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-21 19:41:23.779][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-21 19:41:23.782][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-21 19:41:23.784][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-21 19:41:23.792][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-21 19:41:23.795][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-21 19:41:23.798][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-21 19:41:23.812][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-21 19:41:23.814][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-21 19:41:23.816][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-21 19:41:23.820][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-21 19:41:23.829][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-21 19:41:23.830][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-21 19:41:23.832][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-21 19:41:23.834][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-21 19:41:23.836][biodb::testThat]
biodb.INFO [2025-03-21 19:41:23.842][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-03-21 19:41:23.844][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:41:23.845][biodb::testThat]
biodb.DEBUG[2025-03-21 19:41:23.850][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-21 19:41:23.864][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:41:23.869][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-21 19:41:23.871][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:41:23.874][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-21 19:41:23.879][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[2025-03-21 19:41:23.890][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:41:23.892][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:41:23.895][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-21 19:41:24.274][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-21 19:41:24.625][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:41:24.628][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-03-21 19:41:24.634][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-03-21 19:41:24.646][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-21 19:41:24.648][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-21 19:41:24.650][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-21 19:41:24.651][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-21 19:41:24.652][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:24.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:24.655][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:24.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:24.657][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:24.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-21 19:41:24.663][biodb::testContext]
biodb.INFO [2025-03-21 19:41:24.665][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-21 19:41:24.666][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-03-21 19:41:24.668][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-21 19:41:24.669][biodb::testContext]
biodb.INFO [2025-03-21 19:41:24.672][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-21 19:41:24.674][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-21 19:41:24.680][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-21 19:41:24.681][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-21 19:41:24.683][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-21 19:41:24.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:24.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:24.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:24.688][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-21 19:41:24.689][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-21 19:41:24.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:24.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:24.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:24.694][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-21 19:41:24.695][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-21 19:41:24.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:24.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:24.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:24.700][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-21 19:41:24.701][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-21 19:41:24.703][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-21 19:41:24.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:24.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:24.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:24.707][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-21 19:41:24.709][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-21 19:41:24.710][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-21 19:41:24.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:24.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:24.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:24.715][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-21 19:41:24.717][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-21 19:41:24.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:24.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:24.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:24.721][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-21 19:41:24.723][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-21 19:41:24.724][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-21 19:41:24.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:24.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:24.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:24.729][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-21 19:41:24.730][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-21 19:41:24.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:24.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:24.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:24.735][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-21 19:41:24.737][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-21 19:41:24.738][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-21 19:41:24.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:24.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:24.741][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[2025-03-21 19:41:24.743][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-21 19:41:24.744][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-21 19:41:24.745][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-21 19:41:24.747][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-21 19:41:24.748][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-21 19:41:24.749][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-21 19:41:24.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:24.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:24.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:24.754][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-21 19:41:24.756][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-21 19:41:24.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:24.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:24.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:24.760][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-21 19:41:24.762][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-21 19:41:24.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:24.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:24.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:24.766][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-21 19:41:24.768][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-21 19:41:24.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:24.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:24.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:24.773][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-21 19:41:24.774][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-21 19:41:24.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:24.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:24.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:24.779][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-21 19:41:24.780][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-21 19:41:24.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:24.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:24.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:24.785][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-21 19:41:24.787][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-21 19:41:24.820][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-21 19:41:24.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:24.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:24.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:24.826][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-21 19:41:24.828][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-21 19:41:24.829][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-21 19:41:24.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:24.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:24.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:24.835][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-21 19:41:24.837][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:24.839][self$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[2025-03-21 19:41:24.840][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:24.842][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-21 19:41:24.843][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:24.844][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-21 19:41:24.846][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:24.847][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-21 19:41:24.848][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-21 19:41:24.851][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-21 19:41:24.853][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:24.854][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-21 19:41:24.855][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-21 19:41:24.857][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:24.858][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:24.859][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-21 19:41:24.859][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-21 19:41:24.859][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-21 19:41:24.859][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-21 19:41:24.859][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-21 19:41:24.861][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-21 19:41:24.863][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:24.864][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:24.865][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-21 19:41:24.866][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:24.868][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:24.869][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-21 19:41:24.870][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:24.871][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-21 19:41:24.873][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-21 19:41:24.874][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:24.875][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:24.877][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-21 19:41:24.879][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:24.881][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-21 19:41:24.889][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:24.890][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-21 19:41:24.892][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:24.893][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-21 19:41:24.895][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:24.896][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-21 19:41:24.897][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-21 19:41:24.904][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-21 19:41:24.905][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:24.907][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-21 19:41:24.908][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-21 19:41:24.910][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:24.911][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:24.916][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-21 19:41:24.916][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-21 19:41:24.916][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-21 19:41:24.916][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-21 19:41:24.916][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-21 19:41:24.917][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-21 19:41:24.919][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:24.920][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:24.921][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-21 19:41:24.923][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:24.924][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:24.930][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-21 19:41:24.931][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:24.933][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-21 19:41:24.934][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-21 19:41:24.935][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:24.937][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:24.967][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-21 19:41:24.970][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:24.971][self$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[2025-03-21 19:41:24.973][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:24.978][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-21 19:41:24.979][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:24.981][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-21 19:41:24.982][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:24.983][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-21 19:41:24.985][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-21 19:41:24.986][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-21 19:41:24.997][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:24.999][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-21 19:41:25.000][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-21 19:41:25.002][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:25.003][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:25.004][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:25.009][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-21 19:41:25.010][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:25.012][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:25.013][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-21 19:41:25.015][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:25.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:25.017][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-21 19:41:25.027][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:25.030][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-21 19:41:25.031][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-21 19:41:25.033][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:25.034][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:25.036][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-21 19:41:25.046][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:25.048][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-21 19:41:25.049][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:25.051][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-21 19:41:25.052][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:25.054][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-21 19:41:25.061][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:25.062][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-21 19:41:25.064][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-21 19:41:25.065][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-21 19:41:25.066][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:25.068][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-21 19:41:25.069][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-21 19:41:25.078][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:25.080][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:25.081][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:25.083][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-21 19:41:25.084][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:25.085][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:25.091][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-21 19:41:25.093][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:25.094][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:25.096][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-21 19:41:25.097][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:25.099][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-21 19:41:25.100][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-21 19:41:25.112][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:25.114][self$setPropertyValue]
biodb.DEBUG[2025-03-21 19:41:25.116][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-21 19:41:25.117][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.166][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.DEBUG[2025-03-21 19:41:25.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.278][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.DEBUG[2025-03-21 19:41:25.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.316][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-21 19:41:25.318][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-21 19:41:25.320][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-21 19:41:25.331][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-21 19:41:25.333][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-21 19:41:25.336][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-21 19:41:25.338][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-21 19:41:25.344][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-21 19:41:25.347][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-21 19:41:25.349][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-21 19:41:25.351][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-21 19:41:25.361][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-21 19:41:25.363][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-21 19:41:25.365][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-21 19:41:25.368][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-21 19:41:25.370][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-21 19:41:25.378][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-21 19:41:25.380][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-21 19:41:25.383][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-21 19:41:25.385][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-21 19:41:25.394][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-21 19:41:25.397][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-21 19:41:25.399][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-21 19:41:25.401][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-21 19:41:25.409][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-21 19:41:25.411][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-21 19:41:25.413][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-21 19:41:25.416][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-21 19:41:25.425][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-21 19:41:25.427][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-21 19:41:25.430][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-21 19:41:25.432][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-21 19:41:25.442][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-21 19:41:25.445][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-21 19:41:25.447][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-21 19:41:25.450][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-21 19:41:25.461][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-21 19:41:25.464][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-21 19:41:25.467][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-21 19:41:25.474][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-21 19:41:25.476][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-21 19:41:25.479][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-21 19:41:25.482][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-21 19:41:25.490][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-21 19:41:25.493][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-21 19:41:25.495][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-21 19:41:25.506][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-21 19:41:25.509][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-21 19:41:25.512][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-21 19:41:25.515][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-21 19:41:25.524][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-21 19:41:25.527][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-21 19:41:25.530][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-21 19:41:25.539][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-21 19:41:25.542][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-21 19:41:25.545][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-21 19:41:25.548][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-21 19:41:25.556][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-21 19:41:25.559][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-21 19:41:25.562][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-21 19:41:25.570][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-21 19:41:25.574][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-21 19:41:25.577][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-21 19:41:25.580][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-21 19:41:25.590][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-21 19:41:25.593][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-21 19:41:25.595][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-21 19:41:25.602][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-21 19:41:25.605][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-21 19:41:25.608][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-21 19:41:25.610][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-21 19:41:25.622][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-21 19:41:25.626][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-21 19:41:25.629][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-21 19:41:25.639][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-21 19:41:25.642][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-21 19:41:25.645][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-21 19:41:25.654][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-21 19:41:25.657][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-21 19:41:25.660][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-21 19:41:25.662][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-21 19:41:25.670][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-21 19:41:25.672][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-21 19:41:25.675][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-21 19:41:25.678][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-21 19:41:25.687][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-21 19:41:25.689][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.692][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:25.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:25.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.710][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[2025-03-21 19:41:25.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:25.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:25.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.728][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[2025-03-21 19:41:25.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:25.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:25.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.745][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[2025-03-21 19:41:25.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:25.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:25.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:25.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:25.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.785][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[2025-03-21 19:41:25.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:25.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:25.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.803][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[2025-03-21 19:41:25.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:25.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:25.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:25.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:25.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:25.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:25.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.858][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[2025-03-21 19:41:25.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:25.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:25.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.874][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[2025-03-21 19:41:25.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:25.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:25.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:25.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:25.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.944][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[2025-03-21 19:41:25.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:25.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:25.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.984][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[2025-03-21 19:41:25.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:25.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:25.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:25.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:25.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:25.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:25.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:25.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:26.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:26.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:26.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:26.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:26.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:26.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:26.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:26.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:26.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:26.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:26.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:26.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:26.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:26.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-21 19:41:26.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:26.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:26.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:26.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:26.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:26.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:26.066][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-21 19:41:26.068][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-21 19:41:26.071][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:26.073][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-21 19:41:26.084][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:26.087][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-21 19:41:26.089][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:26.091][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-21 19:41:26.093][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:26.100][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-21 19:41:26.102][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-21 19:41:26.105][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-21 19:41:26.107][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:26.109][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-21 19:41:26.118][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-21 19:41:26.120][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-21 19:41:26.120][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-21 19:41:26.120][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-21 19:41:26.120][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-21 19:41:26.120][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-21 19:41:26.120][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-21 19:41:26.120][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-21 19:41:26.120][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-21 19:41:26.120][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-21 19:41:26.120][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-21 19:41:26.120][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-21 19:41:26.122][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-21 19:41:26.124][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-21 19:41:26.124][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-21 19:41:26.124][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-21 19:41:26.125][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-21 19:41:26.132][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:26.133][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:26.135][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-21 19:41:26.137][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-21 19:41:26.139][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-21 19:41:26.140][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-21 19:41:26.149][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:41:26.149][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-21 19:41:26.151][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-21 19:41:26.154][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-21 19:41:26.156][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-21 19:41:26.159][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-21 19:41:26.159][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-21 19:41:26.168][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-21 19:41:26.172][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-21 19:41:26.174][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-21 19:41:26.183][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-21 19:41:26.187][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-21 19:41:26.190][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-21 19:41:26.205][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-21 19:41:26.207][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-21 19:41:26.210][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-21 19:41:26.221][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-21 19:41:26.224][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-21 19:41:26.226][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-21 19:41:26.234][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-21 19:41:26.237][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-21 19:41:26.240][biodb::testThat]
biodb.INFO [2025-03-21 19:41:26.241][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-03-21 19:41:26.250][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-21 19:41:26.252][biodb::testThat]
biodb.DEBUG[2025-03-21 19:41:26.258][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-21 19:41:26.274][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:41:26.277][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-21 19:41:26.287][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:41:26.291][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-21 19:41:26.305][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-21 19:41:26.320][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-21 19:41:26.323][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-03-21 19:41:26.326][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-21 19:41:26.333][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-03-21 19:41:26.353][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-03-21 19:41:26.356][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-21 19:41:26.360][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-03-21 19:41:26.370][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-21 19:41:26.373][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-21 19:41:26.375][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-21 19:41:26.377][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-21 19:41:26.379][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-21 19:41:26.387][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-21 19:41:26.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:26.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:26.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:26.424][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:26.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:26.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:26.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-21 19:41:26.441][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-03-21 19:41:26.446][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-21 19:41:26.455][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-21 19:41:26.459][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-03-21 19:41:27.675][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-03-21 19:41:28.716][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-21 19:41:28.720][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-03-21 19:41:28.726][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-03-21 19:41:28.730][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-03-21 19:41:28.733][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-21 19:41:28.735][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-21 19:41:28.737][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-21 19:41:28.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-21 19:41:28.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:28.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:28.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:28.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:28.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:28.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-21 19:41:28.760][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:28.762][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:28.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.764][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:28.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:28.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.772][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:41:28.773][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:41:28.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.776][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.778][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-21 19:41:28.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-21 19:41:28.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.783][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:41:28.785][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:41:28.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.787][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.789][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-21 19:41:28.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-21 19:41:28.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.795][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-21 19:41:28.796][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-21 19:41:28.797][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.799][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.801][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-21 19:41:28.802][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-21 19:41:28.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.804][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.806][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:28.808][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:28.809][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.810][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.812][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:28.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-21 19:41:28.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.818][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:41:28.819][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:28.820][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.822][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.823][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-21 19:41:28.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-21 19:41:28.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.829][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:28.830][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:28.832][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.833][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:28.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-21 19:41:28.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.840][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:41:28.842][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:41:28.843][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.844][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.847][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-21 19:41:28.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-21 19:41:28.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.852][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:41:28.854][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:41:28.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.857][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.858][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-21 19:41:28.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-21 19:41:28.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.864][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:41:28.865][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:41:28.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.868][ef$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.870][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-21 19:41:28.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-21 19:41:28.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:28.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:28.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:28.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:28.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:28.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:28.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-21 19:41:28.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-21 19:41:28.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:28.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:28.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:28.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:28.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:28.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:28.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:28.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:28.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:28.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:28.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-21 19:41:28.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-21 19:41:28.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-21 19:41:28.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-21 19:41:28.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-21 19:41:28.964][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-03-21 19:41:28.983][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-21 19:41:28.985][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-21 19:41:28.987][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-21 19:41:28.989][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-21 19:41:28.990][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-21 19:41:28.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-21 19:41:29.001][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-21 19:41:29.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-21 19:41:29.004][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-21 19:41:29.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 385 ]
>
> proc.time()
user system elapsed
22.035 1.342 63.901
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 2.770 | 1.109 | 4.864 | |
| ChebiEntry | 0.368 | 0.017 | 0.399 | |