Pierrick Roger
| Snapshot Date: 2025-03-20 13:40 -0400 (Thu, 20 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 2025-03-21 11:43 -0400 (Fri, 21 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4777 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4458 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 204/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.13.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbChebi |
| Version: 1.13.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.13.0.tar.gz |
| StartedAt: 2025-03-20 19:32:55 -0400 (Thu, 20 Mar 2025) |
| EndedAt: 2025-03-20 19:36:03 -0400 (Thu, 20 Mar 2025) |
| EllapsedTime: 188.1 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 [2025-03-20 19:33:54.137][biodb::testContext]
biodb.INFO [2025-03-20 19:33:54.141][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 19:33:54.142][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-03-20 19:33:54.143][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 19:33:54.144][biodb::testContext]
biodb.INFO [2025-03-20 19:33:54.152][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-20 19:33:54.154][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-20 19:33:54.164][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 19:33:54.166][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-20 19:33:54.167][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-20 19:33:54.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.171][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-20 19:33:54.194][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-20 19:33:54.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.199][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-20 19:33:54.200][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-20 19:33:54.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.205][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-20 19:33:54.207][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-20 19:33:54.208][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-20 19:33:54.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.211][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-20 19:33:54.212][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-20 19:33:54.213][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-20 19:33:54.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.217][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-20 19:33:54.219][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-20 19:33:54.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.222][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-20 19:33:54.224][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-20 19:33:54.225][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-20 19:33:54.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.229][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-20 19:33:54.230][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-20 19:33:54.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.235][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-20 19:33:54.236][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-20 19:33:54.237][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-20 19:33:54.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.241][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-20 19:33:54.243][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-20 19:33:54.244][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-20 19:33:54.244][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-20 19:33:54.245][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-20 19:33:54.247][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-20 19:33:54.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.251][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-20 19:33:54.251][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-20 19:33:54.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.255][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-20 19:33:54.256][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-20 19:33:54.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.261][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-20 19:33:54.262][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-20 19:33:54.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.267][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-20 19:33:54.269][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-20 19:33:54.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.271][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.DEBUG[2025-03-20 19:33:54.272][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-20 19:33:54.273][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-20 19:33:54.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.277][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-20 19:33:54.279][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-20 19:33:54.304][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-20 19:33:54.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.307][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[2025-03-20 19:33:54.308][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-20 19:33:54.309][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-20 19:33:54.310][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-20 19:33:54.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.316][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-20 19:33:54.354][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 19:33:54.382][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-20 19:33:54.384][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 19:33:54.385][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 19:33:54.387][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 19:33:54.388][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 19:33:54.389][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 19:33:54.391][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 19:33:54.392][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 19:33:54.394][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 19:33:54.395][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 19:33:54.396][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-20 19:33:54.398][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 19:33:54.399][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:33:54.400][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 19:33:54.401][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 19:33:54.401][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 19:33:54.401][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 19:33:54.401][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 19:33:54.401][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 19:33:54.403][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 19:33:54.404][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:33:54.405][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:33:54.406][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 19:33:54.407][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:33:54.408][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:33:54.410][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 19:33:54.411][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:33:54.412][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 19:33:54.413][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 19:33:54.415][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 19:33:54.416][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:33:54.418][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-20 19:33:54.420][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 19:33:54.421][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 19:33:54.422][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 19:33:54.423][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 19:33:54.425][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 19:33:54.426][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 19:33:54.427][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 19:33:54.429][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 19:33:54.430][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 19:33:54.431][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 19:33:54.433][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 19:33:54.434][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-20 19:33:54.435][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 19:33:54.436][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:33:54.438][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 19:33:54.439][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 19:33:54.439][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 19:33:54.439][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 19:33:54.439][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 19:33:54.439][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 19:33:54.440][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 19:33:54.442][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:33:54.443][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:33:54.444][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 19:33:54.446][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:33:54.446][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:33:54.448][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 19:33:54.449][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:33:54.450][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 19:33:54.451][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 19:33:54.452][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 19:33:54.453][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:33:54.454][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-20 19:33:54.456][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 19:33:54.457][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-20 19:33:54.458][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 19:33:54.459][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 19:33:54.460][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 19:33:54.461][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 19:33:54.462][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 19:33:54.463][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 19:33:54.464][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 19:33:54.465][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 19:33:54.466][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 19:33:54.467][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-20 19:33:54.467][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 19:33:54.468][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:33:54.469][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 19:33:54.470][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:33:54.471][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 19:33:54.473][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:33:54.474][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:33:54.475][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 19:33:54.475][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:33:54.476][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:33:54.477][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 19:33:54.478][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:33:54.479][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 19:33:54.479][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 19:33:54.480][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 19:33:54.481][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:33:54.483][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-20 19:33:54.485][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 19:33:54.487][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 19:33:54.488][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 19:33:54.489][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 19:33:54.491][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 19:33:54.491][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 19:33:54.492][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 19:33:54.493][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 19:33:54.495][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 19:33:54.496][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 19:33:54.497][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 19:33:54.498][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-20 19:33:54.499][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 19:33:54.501][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:33:54.502][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 19:33:54.503][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:33:54.504][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 19:33:54.505][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:33:54.506][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:33:54.507][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 19:33:54.508][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:33:54.509][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:33:54.510][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 19:33:54.511][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:33:54.512][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 19:33:54.513][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 19:33:54.514][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 19:33:54.515][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:33:54.519][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 19:33:54.520][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.543][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[2025-03-20 19:33:54.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.554][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.DEBUG[2025-03-20 19:33:54.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.559][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[2025-03-20 19:33:54.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.565][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[2025-03-20 19:33:54.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.571][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[2025-03-20 19:33:54.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.576][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[2025-03-20 19:33:54.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.594][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[2025-03-20 19:33:54.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.599][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[2025-03-20 19:33:54.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.604][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[2025-03-20 19:33:54.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.614][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[2025-03-20 19:33:54.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.622][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-20 19:33:54.627][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-20 19:33:54.629][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-20 19:33:54.631][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-20 19:33:54.633][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 19:33:54.635][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-20 19:33:54.636][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-20 19:33:54.638][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-20 19:33:54.640][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-20 19:33:54.642][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-20 19:33:54.644][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 19:33:54.646][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-20 19:33:54.648][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-20 19:33:54.650][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-20 19:33:54.652][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-20 19:33:54.654][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-20 19:33:54.656][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-20 19:33:54.658][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-20 19:33:54.660][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 19:33:54.662][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-20 19:33:54.664][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-20 19:33:54.666][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-20 19:33:54.668][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-20 19:33:54.669][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-20 19:33:54.671][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-20 19:33:54.673][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-20 19:33:54.675][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-20 19:33:54.676][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-20 19:33:54.678][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-20 19:33:54.680][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-20 19:33:54.682][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-20 19:33:54.684][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-20 19:33:54.685][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-20 19:33:54.687][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-20 19:33:54.688][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-20 19:33:54.690][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-20 19:33:54.692][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-20 19:33:54.694][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-20 19:33:54.695][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-20 19:33:54.697][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-20 19:33:54.699][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-20 19:33:54.700][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-20 19:33:54.702][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-20 19:33:54.704][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-20 19:33:54.705][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-20 19:33:54.707][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-20 19:33:54.709][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-20 19:33:54.711][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-20 19:33:54.713][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-20 19:33:54.715][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-20 19:33:54.717][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-20 19:33:54.719][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-20 19:33:54.721][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-20 19:33:54.722][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-20 19:33:54.725][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-20 19:33:54.726][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-20 19:33:54.728][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-20 19:33:54.730][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-20 19:33:54.732][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-20 19:33:54.734][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-20 19:33:54.736][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-20 19:33:54.738][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-20 19:33:54.740][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-20 19:33:54.742][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-20 19:33:54.743][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-20 19:33:54.745][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-20 19:33:54.747][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 19:33:54.749][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 19:33:54.751][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-20 19:33:54.753][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-20 19:33:54.754][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-20 19:33:54.756][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-20 19:33:54.757][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-20 19:33:54.759][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-20 19:33:54.761][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-20 19:33:54.763][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-20 19:33:54.764][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-20 19:33:54.766][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-20 19:33:54.767][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-20 19:33:54.769][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-20 19:33:54.771][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-20 19:33:54.773][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-20 19:33:54.774][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-20 19:33:54.781][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-20 19:33:54.783][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-20 19:33:54.786][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 19:33:54.787][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.789][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.791][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[2025-03-20 19:33:54.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:33:54.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:33:54.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.805][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[2025-03-20 19:33:54.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:33:54.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:33:54.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:33:54.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:33:54.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.829][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[2025-03-20 19:33:54.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:33:54.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:33:54.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.837][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[2025-03-20 19:33:54.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:33:54.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:33:54.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:33:54.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:33:54.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:33:54.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:33:54.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.858][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[2025-03-20 19:33:54.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:33:54.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:33:54.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:33:54.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:33:54.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.874][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[2025-03-20 19:33:54.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:33:54.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:33:54.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:33:54.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:33:54.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:33:54.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:33:54.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:33:54.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:33:54.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:33:54.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:33:54.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:33:54.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:33:54.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:33:54.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:33:54.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:33:54.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:33:54.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:33:54.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:54.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:54.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:54.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:33:54.936][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-20 19:33:54.948][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-20 19:33:54.951][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 19:33:54.952][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-20 19:33:54.954][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 19:33:54.955][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 19:33:54.957][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 19:33:54.958][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 19:33:54.960][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-20 19:33:54.961][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-20 19:33:54.962][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-20 19:33:54.963][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 19:33:54.965][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 19:33:54.966][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-20 19:33:54.967][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 19:33:54.968][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-20 19:33:54.968][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-20 19:33:54.968][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-20 19:33:54.968][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-20 19:33:54.968][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-20 19:33:54.968][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-20 19:33:54.968][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-20 19:33:54.968][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-20 19:33:54.968][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-20 19:33:54.968][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-20 19:33:54.968][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-20 19:33:54.970][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-20 19:33:54.971][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 19:33:54.971][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 19:33:54.971][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 19:33:54.972][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-20 19:33:54.973][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:33:54.974][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:33:54.975][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 19:33:54.976][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:33:54.977][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:33:54.977][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 19:33:54.978][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:33:54.978][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-20 19:33:54.980][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 19:33:54.981][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 19:33:54.982][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-20 19:33:54.983][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-20 19:33:54.983][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-20 19:33:54.992][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 19:33:54.995][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 19:33:54.997][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-20 19:33:55.000][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 19:33:55.002][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 19:33:55.005][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 19:33:55.040][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-20 19:33:55.042][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-20 19:33:55.048][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-20 19:33:55.053][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-20 19:33:55.100][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 19:33:55.102][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 19:33:55.103][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-20 19:33:55.104][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-20 19:33:55.114][biodb::testThat]
biodb.INFO [2025-03-20 19:33:55.115][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-03-20 19:33:55.116][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:33:55.117][biodb::testThat]
biodb.TRACE[2025-03-20 19:33:55.121][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[2025-03-20 19:33:55.123][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:33:55.126][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:33:55.136][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:33:55.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:33:55.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:33:55.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:55.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:55.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:55.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:33:55.168][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:55.170][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:55.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.173][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:55.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:55.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.193][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:33:55.195][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:33:55.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.197][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.231][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:33:55.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:33:55.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.238][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:33:55.239][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:33:55.240][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.241][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.243][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:33:55.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:33:55.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.247][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:33:55.248][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:33:55.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.250][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.251][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:33:55.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:33:55.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.255][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:33:55.256][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:33:55.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.257][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.259][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:33:55.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:33:55.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.263][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:33:55.264][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:33:55.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.266][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.268][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:33:55.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:33:55.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.272][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:33:55.273][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:55.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.276][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.277][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:33:55.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:55.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.282][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:55.283][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:55.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.285][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.287][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:55.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:55.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.291][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:33:55.292][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:33:55.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.294][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.306][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:33:55.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:33:55.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.312][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:33:55.314][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:33:55.315][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.316][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.317][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:33:55.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:33:55.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.321][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:33:55.322][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:33:55.323][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.325][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.326][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:33:55.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:33:55.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:55.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:55.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.342][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:55.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:55.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:55.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:55.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:55.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:55.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:55.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:55.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:55.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:55.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:55.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:55.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:33:55.412][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-03-20 19:33:55.416][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:33:55.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:33:55.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.421][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:33:55.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:33:55.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.447][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:33:55.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:33:55.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.456][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:33:55.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:33:55.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:55.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:55.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.466][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:55.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:55.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.471][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-20 19:33:55.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-20 19:33:55.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.475][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-20 19:33:55.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-20 19:33:55.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.479][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-20 19:33:55.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-20 19:33:55.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.484][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-20 19:33:55.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-20 19:33:55.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:55.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:55.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:55.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:55.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:55.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:55.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:55.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:55.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:55.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:55.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:55.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:55.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:55.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:55.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:55.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:55.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:55.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:55.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:55.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:55.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.602][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:55.603][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:55.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.605][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:55.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:55.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.649][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.651][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.652][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.653][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:33:55.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.670][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:33:55.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:33:55.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.674][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:33:55.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:33:55.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.679][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:33:55.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:33:55.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.683][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:33:55.684][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:33:55.684][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.685][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.686][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:33:55.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:33:55.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.702][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:33:55.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:33:55.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.707][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:33:55.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:33:55.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.711][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:33:55.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:33:55.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.715][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:33:55.716][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:33:55.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.718][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.719][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:33:55.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:33:55.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:55.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:55.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.740][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:55.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:55.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:55.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:55.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.749][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:55.750][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:55.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.751][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:55.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:55.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:55.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:55.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:55.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:55.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:55.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:55.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.782][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:55.784][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:55.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.786][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:55.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:55.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.804][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:33:55.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:33:55.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.810][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:33:55.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:33:55.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.816][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:33:55.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:33:55.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.822][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:33:55.823][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:33:55.824][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.825][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.833][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:33:55.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:33:55.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.849][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-20 19:33:55.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:33:55.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.855][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-20 19:33:55.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:33:55.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.859][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-20 19:33:55.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:33:55.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.864][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-20 19:33:55.865][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:33:55.866][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.867][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.868][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-20 19:33:55.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:33:55.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.884][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:33:55.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:33:55.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.890][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:33:55.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:33:55.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.894][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:33:55.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:33:55.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.899][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:33:55.900][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:33:55.902][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.903][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.904][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:33:55.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:33:55.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.920][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:33:55.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:33:55.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.926][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:33:55.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:33:55.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.930][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:33:55.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:33:55.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.934][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:33:55.935][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:33:55.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.937][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.939][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:33:55.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:33:55.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.955][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:33:55.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:33:55.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.961][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:33:55.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:33:55.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.965][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:33:55.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:33:55.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.970][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:33:55.972][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:33:55.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.974][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.976][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:33:55.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:33:55.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.991][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:33:55.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:33:55.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:55.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:55.996][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:33:55.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:33:55.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.001][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:33:56.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:33:56.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.005][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:33:56.005][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:33:56.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.007][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.008][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:33:56.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:33:56.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.028][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:56.030][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:56.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.033][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.040][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:33:56.041][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:33:56.043][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.044][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.051][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:33:56.052][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:33:56.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.054][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.061][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:33:56.062][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:33:56.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.064][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.071][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:33:56.072][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:33:56.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.075][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.082][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:33:56.083][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:33:56.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.085][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.092][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:56.094][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:56.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.097][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.104][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:56.105][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:56.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.107][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.113][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-20 19:33:56.114][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:33:56.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.116][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.122][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:33:56.124][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:33:56.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.126][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.133][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:33:56.135][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:33:56.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.137][ef$get] fields variable is a list.
biodb.INFO [2025-03-20 19:33:56.148][biodb::testThat]
biodb.INFO [2025-03-20 19:33:56.149][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-20 19:33:56.150][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:33:56.150][biodb::testThat]
biodb.DEBUG[2025-03-20 19:33:56.168][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-03-20 19:33:56.175][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:33:56.181][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-03-20 19:33:56.183][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:33:56.185][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-03-20 19:33:56.187][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:33:56.225][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:33:56.227][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:33:56.229][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:33:56.230][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:33:56.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:33:56.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:33:56.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:33:56.241][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:33:56.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:33:56.245][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:56.246][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:56.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.248][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:56.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:56.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.275][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:33:56.277][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:33:56.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.279][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.280][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:33:56.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:33:56.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.285][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:33:56.286][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:33:56.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.288][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.289][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:33:56.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:33:56.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.293][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:33:56.295][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:33:56.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.297][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.299][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:33:56.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:33:56.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.304][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:33:56.305][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:33:56.306][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.307][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.308][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:33:56.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:33:56.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.312][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:33:56.313][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:33:56.315][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.316][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.317][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:33:56.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:33:56.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.321][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:33:56.322][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:56.323][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.324][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.326][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:33:56.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:56.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.331][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:56.332][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:56.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.334][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:56.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:56.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.340][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:33:56.341][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:33:56.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.342][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.344][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:33:56.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:33:56.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.349][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:33:56.350][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:33:56.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.352][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.354][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:33:56.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:33:56.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.359][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:33:56.360][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:33:56.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.363][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.364][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:33:56.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:33:56.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:33:56.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:33:56.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:33:56.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:33:56.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:56.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:56.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:33:56.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:33:56.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:56.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:56.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:56.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:56.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:56.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:56.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:56.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:56.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:56.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:56.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:33:56.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:33:56.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:33:56.428][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-03-20 19:33:56.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-20 19:33:56.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-20 19:33:56.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-20 19:33:56.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-20 19:33:56.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-20 19:33:56.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-20 19:33:56.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-20 19:33:56.453][biodb::testThat]
biodb.INFO [2025-03-20 19:33:56.454][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-20 19:33:56.456][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:33:56.457][biodb::testThat]
biodb.TRACE[2025-03-20 19:33:56.462][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:33:56.463][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:33:56.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.465][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:33:56.467][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-03-20 19:33:56.504][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:33:56.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:33:56.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.509][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:33:56.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:33:56.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:56.514][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:33:56.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:33:56.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:56.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:33:56.520][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-03-20 19:33:56.524][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-20 19:33:56.548][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:33:56.576][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-20 19:33:56.578][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:33:56.580][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-20 19:33:56.607][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[2025-03-20 19:33:56.611][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:33:56.613][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:33:56.615][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-20 19:33:57.383][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-20 19:33:57.798][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:33:57.801][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-03-20 19:33:57.822][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-03-20 19:33:57.826][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-03-20 19:33:57.842][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:57.844][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:33:57.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:57.846][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:57.847][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:57.848][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:57.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:57.850][ef$get] fields variable is a list.
biodb.INFO [2025-03-20 19:33:57.855][biodb::testThat]
biodb.INFO [2025-03-20 19:33:57.857][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-03-20 19:33:57.858][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:33:57.859][biodb::testThat]
biodb.TRACE[2025-03-20 19:33:57.891][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:33:57.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:33:57.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:57.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:57.897][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:33:57.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:33:57.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:57.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:57.914][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:33:57.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:33:57.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:57.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:33:57.983][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 19:33:57.987][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:33:57.989][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-20 19:33:57.991][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:33:57.993][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-03-20 19:33:58.017][biodb::testThat]
biodb.INFO [2025-03-20 19:33:58.018][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-03-20 19:33:58.020][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:33:58.021][biodb::testThat]
biodb.TRACE[2025-03-20 19:33:58.056][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:33:58.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:33:58.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:58.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:58.060][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:33:58.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:33:58.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:58.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:58.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:33:58.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:33:58.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:58.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:58.071][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:33:58.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:33:58.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:58.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:58.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:58.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:58.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:58.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:58.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:58.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:58.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:58.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:58.082][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-20 19:33:58.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-20 19:33:58.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:58.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:58.087][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-20 19:33:58.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-20 19:33:58.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:58.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:58.092][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-20 19:33:58.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-20 19:33:58.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:58.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:58.098][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-20 19:33:58.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-20 19:33:58.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:58.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:58.125][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:33:58.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:33:58.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:58.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:58.130][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:33:58.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:33:58.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:58.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:58.136][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:33:58.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:33:58.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:58.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:58.141][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:33:58.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:33:58.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:58.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:58.146][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:58.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:58.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:58.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:58.151][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:58.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:33:58.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:58.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:58.156][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-20 19:33:58.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-20 19:33:58.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:58.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:58.162][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-20 19:33:58.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-20 19:33:58.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:58.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:58.167][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-20 19:33:58.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-20 19:33:58.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:58.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:33:58.171][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-20 19:33:58.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-20 19:33:58.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:33:58.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-20 19:33:58.194][biodb::testThat]
biodb.INFO [2025-03-20 19:33:58.196][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-20 19:33:58.197][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:33:58.198][biodb::testThat]
biodb.INFO [2025-03-20 19:33:58.211][biodb::testThat]
biodb.INFO [2025-03-20 19:33:58.213][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-20 19:33:58.214][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:33:58.216][biodb::testThat]
biodb.INFO [2025-03-20 19:33:58.228][biodb::testThat]
biodb.INFO [2025-03-20 19:33:58.229][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-20 19:33:58.231][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:33:58.233][biodb::testThat]
biodb.DEBUG[2025-03-20 19:33:58.238][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-03-20 19:33:58.916][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-03-20 19:34:01.489][biodb::testThat]
biodb.INFO [2025-03-20 19:34:01.490][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-20 19:34:01.492][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:34:01.493][biodb::testThat]
biodb.DEBUG[2025-03-20 19:34:01.881][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[2025-03-20 19:34:02.263][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:02.264][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:02.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:02.267][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:02.268][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:02.270][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:02.271][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:02.272][ef$get] fields variable is a list.
biodb.INFO [2025-03-20 19:34:02.274][biodb::testThat]
biodb.INFO [2025-03-20 19:34:02.275][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2025-03-20 19:34:02.276][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:34:02.278][biodb::testThat]
biodb.TRACE[2025-03-20 19:34:02.292][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:02.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:02.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:02.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:02.298][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:02.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:02.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:02.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:02.302][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:02.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:02.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:02.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:02.407][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 19:34:02.412][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:34:02.414][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-20 19:34:02.416][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:34:02.418][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-20 19:34:02.502][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 19:34:02.507][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:34:02.509][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-20 19:34:02.511][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:34:02.513][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-03-20 19:34:02.533][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-20 19:34:02.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-20 19:34:02.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:02.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:02.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:02.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:02.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:02.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:02.552][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:02.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:02.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:02.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:02.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:02.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:02.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:02.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:02.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:02.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:02.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:02.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:02.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:02.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:02.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:02.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:02.581][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 19:34:02.586][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:34:02.588][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-20 19:34:02.590][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:34:02.599][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-20 19:34:02.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:02.604][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:02.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:02.611][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:02.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:02.613][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:02.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:02.615][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-03-20 19:34:02.676][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:02.679][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-03-20 19:34:02.681][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:02.682][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:02.684][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:02.685][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:02.686][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:02.687][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:02.691][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:02.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:02.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:02.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:02.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:02.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:02.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:02.703][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-03-20 19:34:02.730][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:02.732][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:02.753][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-03-20 19:34:03.093][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-03-20 19:34:04.798][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:04.800][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-03-20 19:34:04.805][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-03-20 19:34:04.809][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-03-20 19:34:04.811][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:04.812][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:04.814][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:04.816][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:04.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:04.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:04.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:04.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:04.829][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:04.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:04.834][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:04.835][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:04.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.838][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:04.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:04.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.845][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:04.847][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:04.848][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.849][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.851][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:04.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:04.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.856][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:04.857][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:04.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.860][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.862][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:04.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:04.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.866][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:04.867][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:04.868][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.869][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.871][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:04.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:04.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.888][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:04.889][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:04.890][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.892][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:04.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:04.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.898][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:04.900][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:04.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.902][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.903][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:04.904][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:04.905][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.907][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.908][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:04.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:04.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.912][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:04.913][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:04.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.915][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:04.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:04.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.922][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:04.923][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:04.924][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.925][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.927][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:04.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:04.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.931][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:04.932][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:04.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.934][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.935][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:04.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:04.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.940][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:04.941][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:04.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.944][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.945][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:04.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:04.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.950][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:04.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:04.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:04.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:04.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:04.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:04.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.963][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:04.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:04.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:04.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:04.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:04.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:04.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:04.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:04.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:04.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:04.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:04.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:04.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:04.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:04.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:04.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:04.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:05.001][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-03-20 19:34:05.015][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:05.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:05.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:05.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:05.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.024][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:05.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:05.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:05.029][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 19:34:05.034][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:34:05.035][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-20 19:34:05.037][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:34:05.039][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-20 19:34:05.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:05.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:05.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:05.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:05.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:05.069][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:05.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:05.071][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:05.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:05.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:05.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:05.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:05.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:05.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:05.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:05.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:05.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:05.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:05.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:05.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:05.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:05.100][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-03-20 19:34:05.102][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:05.104][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-03-20 19:34:05.106][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:05.107][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:05.109][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:05.110][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:05.111][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:05.113][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:05.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:05.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:05.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:05.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:05.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:05.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:05.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:05.154][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-03-20 19:34:05.158][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:05.159][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:05.161][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-03-20 19:34:05.501][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-03-20 19:34:05.841][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:05.844][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-03-20 19:34:05.848][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-03-20 19:34:05.852][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-03-20 19:34:05.854][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:05.856][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:05.858][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:05.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:05.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:05.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:05.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:05.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:05.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:05.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:05.874][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:05.876][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:05.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.878][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:05.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:05.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.884][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:05.885][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:05.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.887][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.888][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:05.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:05.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.892][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:05.893][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:05.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.895][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.896][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:05.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:05.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.901][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:05.902][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:05.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.904][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.905][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:05.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:05.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.909][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:05.910][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:05.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.912][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.914][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:05.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:05.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.929][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:05.930][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:05.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.933][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.934][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:05.935][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:05.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.937][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.939][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:05.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:05.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.943][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:05.945][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:05.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.947][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:05.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:05.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.954][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:05.956][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:05.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.958][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.960][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:05.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:05.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.966][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:05.967][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:05.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.969][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.971][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:05.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:05.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.976][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:05.978][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:05.979][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.980][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.982][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:05.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:05.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:05.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:05.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:05.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:05.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:05.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:05.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:05.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:05.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:06.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:06.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:06.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:06.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:06.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:06.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:06.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:06.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:06.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:06.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:06.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:06.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:06.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:06.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:06.031][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-03-20 19:34:06.033][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:06.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:06.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.037][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:06.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:06.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:06.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:06.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:06.108][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 19:34:06.112][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:34:06.114][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-20 19:34:06.115][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:34:06.116][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-20 19:34:06.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:06.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:06.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:06.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:06.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:06.129][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:06.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:06.130][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:06.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:06.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.134][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:06.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:06.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.138][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:06.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:06.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:06.142][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:06.143][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:06.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:06.151][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:06.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:06.154][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:06.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:06.157][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-03-20 19:34:06.158][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:06.160][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-03-20 19:34:06.161][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:06.163][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:06.164][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:06.165][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:06.166][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:06.167][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:06.171][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:06.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:06.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:06.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:06.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:06.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:06.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:06.186][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-03-20 19:34:06.189][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:06.190][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:06.192][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-03-20 19:34:06.528][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-03-20 19:34:06.866][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:06.870][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-03-20 19:34:06.886][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-03-20 19:34:06.891][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-03-20 19:34:06.893][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:06.895][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:06.897][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:06.899][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:06.900][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:06.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:06.908][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:06.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:06.911][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:06.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:06.916][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:06.917][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:06.918][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.919][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:06.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:06.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.925][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:06.927][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:06.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.929][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.931][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:06.932][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:06.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.934][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.936][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:06.936][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:06.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.938][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.940][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:06.941][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:06.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.943][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.944][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:06.946][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:06.947][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.948][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.950][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:06.951][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:06.952][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.953][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.955][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:06.956][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:06.958][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.959][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.961][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:06.962][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:06.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.964][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.966][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:06.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:06.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.971][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:06.973][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:06.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.975][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.976][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:06.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:06.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.982][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:06.984][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:06.985][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.986][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:06.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:06.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:06.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:06.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:06.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:06.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:07.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:07.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:07.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:07.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:07.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:07.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:07.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:07.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:07.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:07.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:07.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:07.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:07.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:07.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:07.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:07.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:07.043][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-03-20 19:34:07.044][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:07.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:07.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:07.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:07.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.054][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:07.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:07.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:07.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:07.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:07.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:07.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:07.069][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:07.070][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:07.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:07.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:07.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:07.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:07.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:07.085][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-03-20 19:34:07.087][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:07.089][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-03-20 19:34:07.090][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:07.091][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:07.092][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:07.094][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:07.095][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:07.097][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:07.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:07.101][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:07.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:07.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:07.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:07.112][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:07.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:07.115][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-03-20 19:34:07.119][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:07.120][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:07.122][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-03-20 19:34:07.460][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-03-20 19:34:07.797][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:07.800][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-03-20 19:34:07.805][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-03-20 19:34:07.809][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-03-20 19:34:07.812][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:07.813][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:07.815][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:07.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:07.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:07.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:07.835][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:07.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:07.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:07.838][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.TRACE[2025-03-20 19:34:07.841][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:07.842][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:07.843][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.844][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:07.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:07.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.849][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:07.850][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:07.851][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.852][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.853][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:07.854][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:07.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.857][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.858][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:07.860][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:07.861][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.863][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.864][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:07.865][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:07.866][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.867][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.869][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:07.871][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:07.872][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.873][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.875][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:07.876][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:07.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.879][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.880][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:07.882][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:07.883][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.884][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.886][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:07.887][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:07.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.890][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.892][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:07.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:07.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.897][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:07.898][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:07.899][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.900][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.901][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:07.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:07.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.906][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:07.907][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:07.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.909][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:07.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:07.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:07.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:07.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:07.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:07.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:07.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:07.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:07.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:07.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:07.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:07.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:07.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:07.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:07.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:07.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:07.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:07.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:07.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:07.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:07.965][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-03-20 19:34:07.966][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:07.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:07.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.971][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:07.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:07.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:07.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:07.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:07.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:07.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:07.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:07.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:07.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:07.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:07.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:07.991][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:07.992][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:07.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:07.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:08.001][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:08.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:08.004][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-03-20 19:34:08.005][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:08.007][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-03-20 19:34:08.009][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:08.010][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:08.011][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:08.012][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:08.013][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:08.014][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:08.017][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:08.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:08.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:08.025][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:08.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:08.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:08.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:08.031][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-03-20 19:34:08.035][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:08.035][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:08.037][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-03-20 19:34:09.753][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-03-20 19:34:10.096][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:10.099][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-03-20 19:34:10.104][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-03-20 19:34:10.107][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-03-20 19:34:10.109][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:10.111][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:10.113][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:10.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:10.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:10.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:10.124][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:10.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:10.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:10.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:10.130][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:10.132][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:10.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.144][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:10.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:10.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.150][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:10.152][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:10.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.154][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.155][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:10.156][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:10.157][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.158][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.159][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:10.161][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:10.162][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.163][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.165][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:10.166][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:10.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.168][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.170][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:10.171][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:10.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.173][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.174][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:10.175][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:10.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.177][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.178][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:10.180][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:10.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.182][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.184][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:10.185][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:10.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.186][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.188][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:10.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:10.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.192][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:10.193][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:10.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.195][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.196][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:10.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:10.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.200][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:10.201][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:10.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.203][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:10.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:10.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:10.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:10.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:10.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:10.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:10.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:10.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:10.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:10.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:10.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:10.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:10.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:10.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:10.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:10.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:10.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:10.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:10.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:10.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:10.262][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-03-20 19:34:10.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:10.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:10.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:10.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:10.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:10.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:10.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:10.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:10.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:10.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:10.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:10.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:10.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:10.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:10.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:10.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:10.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:10.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:10.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:10.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:10.299][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-03-20 19:34:10.300][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:10.302][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-03-20 19:34:10.303][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:10.304][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:10.305][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:10.306][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:10.308][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:10.309][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:10.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:10.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:10.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:10.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:10.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:10.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:10.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:10.327][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-03-20 19:34:10.331][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:10.332][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:10.334][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-03-20 19:34:10.899][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-03-20 19:34:11.248][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:11.250][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-03-20 19:34:11.255][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-03-20 19:34:11.258][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-03-20 19:34:11.261][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:11.263][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:11.264][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:11.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:11.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:11.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:11.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:11.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:11.278][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:11.279][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[2025-03-20 19:34:11.281][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:11.282][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:11.283][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.284][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:11.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:11.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.291][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:11.292][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:11.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.295][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.306][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:11.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:11.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.313][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:11.314][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:11.315][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.316][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.317][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:11.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:11.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.322][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:11.323][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:11.324][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.325][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.326][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:11.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:11.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.330][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:11.331][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:11.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.333][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.334][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:11.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:11.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.340][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:11.340][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:11.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.343][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.344][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:11.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:11.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.348][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:11.349][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:11.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.351][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.352][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:11.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:11.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.357][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:11.358][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:11.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.360][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.362][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:11.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:11.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.366][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:11.367][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:11.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.369][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.371][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:11.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:11.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.376][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:11.377][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:11.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.379][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.381][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:11.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:11.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.385][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:11.387][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:11.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.389][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.391][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:11.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:11.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:11.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:11.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:11.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:11.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:11.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:11.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:11.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:11.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:11.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:11.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:11.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:11.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:11.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:11.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:11.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:11.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:11.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:11.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:11.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:11.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:11.451][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-03-20 19:34:11.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:11.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:11.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.457][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:11.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:11.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:11.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:11.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:11.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:11.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:11.466][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:11.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:11.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:11.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:11.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:11.477][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:11.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:11.479][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-03-20 19:34:11.480][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:11.482][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-03-20 19:34:11.484][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:11.485][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:11.486][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:11.487][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:11.489][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:11.490][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:11.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:11.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:11.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:11.503][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:11.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:11.505][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:11.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:11.507][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-03-20 19:34:11.510][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:11.511][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:11.512][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-03-20 19:34:11.850][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-03-20 19:34:13.597][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:13.600][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-03-20 19:34:13.605][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-03-20 19:34:13.609][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-03-20 19:34:13.611][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:13.612][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:13.614][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:13.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:13.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:13.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:13.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:13.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:13.634][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:13.640][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.TRACE[2025-03-20 19:34:13.642][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:13.644][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:13.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.647][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:13.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:13.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.653][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:13.655][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:13.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.657][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.658][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:13.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:13.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.663][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:13.664][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:13.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.666][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.668][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:13.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:13.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.672][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:13.674][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:13.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.676][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.678][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:13.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:13.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.682][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:13.683][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:13.684][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.685][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.687][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:13.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:13.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.692][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:13.693][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:13.694][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.695][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.696][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:13.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:13.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.702][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:13.703][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:13.705][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.706][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.708][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:13.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:13.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.713][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:13.714][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:13.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.717][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:13.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:13.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.723][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:13.724][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:13.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.727][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.729][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:13.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:13.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.734][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:13.736][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:13.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.738][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.740][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:13.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:13.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.745][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:13.747][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:13.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.749][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.751][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:13.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:13.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:13.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:13.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:13.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:13.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:13.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:13.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:13.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:13.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:13.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:13.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:13.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:13.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:13.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:13.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:13.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:13.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:13.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:13.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:13.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:13.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:13.818][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-03-20 19:34:13.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:13.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:13.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.825][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:13.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:13.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:13.830][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:13.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:13.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:13.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:13.835][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:13.836][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:13.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:13.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:13.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:13.847][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:13.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:13.850][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-03-20 19:34:13.851][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:13.853][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-03-20 19:34:13.855][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:13.857][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:13.858][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:13.860][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:13.861][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:13.862][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:13.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:13.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:13.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:13.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:13.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:13.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:13.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:13.881][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-03-20 19:34:13.884][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:13.885][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:13.887][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-03-20 19:34:14.225][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-03-20 19:34:16.070][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:16.073][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-03-20 19:34:16.084][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-03-20 19:34:16.092][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-03-20 19:34:16.095][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:16.096][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:16.098][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:16.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:16.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:16.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:16.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:16.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:16.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:16.114][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[2025-03-20 19:34:16.117][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:16.118][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:16.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.120][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:16.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:16.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.126][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:16.127][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:16.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.129][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.131][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:16.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:16.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.135][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:16.136][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:16.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.138][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.140][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:16.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:16.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.144][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:16.145][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:16.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.147][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.149][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:16.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:16.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.153][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:16.154][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:16.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.157][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.158][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:16.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:16.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.163][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:16.164][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:16.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.167][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.168][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:16.170][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:16.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.172][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.173][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:16.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:16.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.178][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:16.180][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:16.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.182][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:16.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:16.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.189][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:16.191][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:16.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.193][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.194][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:16.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:16.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.199][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:16.200][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:16.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.202][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.204][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:16.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:16.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.216][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:16.217][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:16.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.220][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.222][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:16.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:16.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:16.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:16.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:16.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:16.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:16.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:16.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.240][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:16.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:16.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:16.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:16.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:16.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:16.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:16.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:16.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:16.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:16.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:16.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:16.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:16.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:16.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:16.272][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-03-20 19:34:16.273][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:16.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:16.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:16.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:16.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:16.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:16.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:16.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:16.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:16.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:16.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:16.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:16.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:16.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:16.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:16.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:16.298][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-03-20 19:34:16.299][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:16.300][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-03-20 19:34:16.302][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:16.303][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:16.304][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:16.306][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:16.307][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:16.308][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:16.312][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:16.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:16.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:16.320][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:16.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:16.322][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:16.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:16.325][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-03-20 19:34:16.336][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:16.338][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:16.340][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-03-20 19:34:17.702][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-03-20 19:34:18.047][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:18.049][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-03-20 19:34:18.053][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-03-20 19:34:18.056][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-03-20 19:34:18.059][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:18.061][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:18.062][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:18.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:18.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:18.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:18.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:18.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:18.076][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:18.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:18.080][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:18.082][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:18.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.084][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:18.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:18.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.090][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:18.091][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:18.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.093][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.095][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:18.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:18.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.101][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:18.102][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:18.103][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.104][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.105][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:18.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:18.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.112][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:18.113][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:18.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.116][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.117][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:18.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:18.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.121][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:18.122][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:18.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.124][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.125][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:18.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:18.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.129][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:18.131][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:18.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.134][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.136][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:18.137][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:18.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.140][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.141][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:18.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:18.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.145][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:18.147][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:18.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.149][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:18.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:18.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.156][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:18.157][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:18.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.159][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.172][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:18.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:18.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.176][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:18.177][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:18.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.179][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.181][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:18.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:18.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.186][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:18.187][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:18.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.189][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.190][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:18.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:18.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.196][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:18.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:18.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.201][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:18.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:18.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:18.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:18.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:18.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:18.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:18.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:18.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:18.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:18.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:18.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:18.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:18.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:18.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:18.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:18.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:18.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:18.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:18.244][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-03-20 19:34:18.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:18.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:18.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:18.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:18.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:18.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:18.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:18.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:18.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:18.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:18.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:18.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:18.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:18.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:18.271][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:18.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:18.274][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-03-20 19:34:18.275][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:18.277][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-03-20 19:34:18.279][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:18.280][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:18.282][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:18.283][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:18.284][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:18.285][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:18.299][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:18.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:18.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:18.309][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:18.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:18.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:18.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:18.314][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-03-20 19:34:18.318][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:18.319][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:18.321][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-03-20 19:34:18.686][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-03-20 19:34:19.029][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:19.031][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-03-20 19:34:19.037][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-03-20 19:34:19.041][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-03-20 19:34:19.043][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:19.045][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:19.046][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:19.049][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:19.050][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:19.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:19.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:19.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:19.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:19.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:19.071][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:19.073][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:19.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.076][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:19.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:19.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.082][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:19.083][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:19.085][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.086][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.088][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:19.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:19.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.093][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:19.095][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:19.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.097][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.099][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:19.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:19.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.104][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:19.106][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:19.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.108][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.110][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:19.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:19.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.115][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:19.117][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:19.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.119][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.121][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:19.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:19.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.126][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:19.128][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:19.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.130][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.131][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:19.133][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:19.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.135][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.136][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:19.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:19.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.152][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:19.154][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:19.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.157][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:19.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:19.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.165][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:19.166][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:19.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.169][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.170][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:19.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:19.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.176][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:19.177][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:19.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.179][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.180][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:19.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:19.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.186][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:19.187][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:19.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.190][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.192][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:19.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:19.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:19.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:19.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.201][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:19.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:19.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:19.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:19.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:19.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:19.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:19.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:19.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:19.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:19.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:19.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:19.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:19.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:19.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:19.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:19.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:19.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:19.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:19.249][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-03-20 19:34:19.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:19.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:19.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:19.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:19.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:19.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:19.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:19.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:19.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:19.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:19.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:19.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:19.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:19.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:19.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:19.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:19.289][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-03-20 19:34:19.290][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:19.293][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-03-20 19:34:19.294][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:19.296][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:19.297][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:19.298][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:19.300][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:19.300][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:19.303][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:19.304][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:19.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:19.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:19.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:19.316][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:19.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:19.319][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-03-20 19:34:19.323][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:19.324][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:19.327][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-03-20 19:34:21.420][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-03-20 19:34:21.763][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:21.765][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-03-20 19:34:21.770][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-03-20 19:34:21.773][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-03-20 19:34:21.775][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:21.776][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:21.777][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:21.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:21.779][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:21.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:21.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:21.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:21.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:21.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:21.791][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:21.792][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:21.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.794][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:21.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:21.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.799][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:21.800][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:21.801][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.802][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.803][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:21.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:21.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.807][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:21.808][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:21.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.809][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.811][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:21.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:21.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.816][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:21.817][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:21.818][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.819][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.821][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:21.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:21.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.826][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:21.827][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:21.828][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.830][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.831][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:21.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:21.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.848][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:21.849][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:21.850][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.851][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.852][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:21.853][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:21.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.855][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.857][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:21.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:21.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.862][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:21.863][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:21.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.865][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:21.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:21.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.869][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:21.870][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:21.872][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.873][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.875][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:21.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:21.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.881][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:21.881][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:21.882][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.883][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.885][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:21.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:21.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.889][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:21.890][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:21.891][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.892][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.894][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:21.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:21.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:21.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:21.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.901][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:21.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:21.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:21.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:21.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:21.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:21.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:21.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:21.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:21.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:21.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:21.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:21.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:21.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:21.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:21.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:21.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:21.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:21.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:21.938][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-03-20 19:34:21.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:21.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:21.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:21.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:21.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:21.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:21.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:21.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:21.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:21.958][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:21.959][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:21.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:21.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:21.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:21.969][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:21.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:21.971][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-03-20 19:34:21.972][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:21.973][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-03-20 19:34:21.974][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:21.975][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:21.976][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:21.977][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:21.978][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:21.979][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:21.982][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:21.983][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:21.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:21.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:21.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:21.992][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:21.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:21.995][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-03-20 19:34:21.998][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:21.999][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:22.001][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-03-20 19:34:22.337][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-03-20 19:34:22.679][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:22.683][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-03-20 19:34:22.686][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-03-20 19:34:22.689][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-03-20 19:34:22.691][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:22.692][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:22.693][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:22.695][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:22.696][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:22.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:22.702][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:22.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:22.704][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:22.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:22.707][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:22.708][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:22.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.710][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:22.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:22.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.716][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:22.717][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:22.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.718][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.720][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:22.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:22.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.723][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:22.724][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:22.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.726][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.727][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:22.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:22.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.738][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:22.743][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:22.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.745][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.747][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:22.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:22.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.751][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:22.751][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:22.753][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.753][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.755][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:22.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:22.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.760][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:22.761][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:22.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.763][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.764][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:22.766][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:22.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.768][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.769][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:22.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:22.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.774][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:22.774][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:22.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.776][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:22.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:22.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.782][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:22.784][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:22.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.786][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.788][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:22.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:22.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.793][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:22.794][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:22.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.796][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.798][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:22.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:22.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.802][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:22.803][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:22.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.805][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.806][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:22.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:22.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:22.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:22.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:22.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:22.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:22.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:22.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:22.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:22.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:22.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:22.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:22.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:22.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:22.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:22.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:22.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:22.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:22.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:22.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:22.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:22.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:22.866][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-03-20 19:34:22.867][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:22.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:22.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.873][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:22.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:22.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:22.879][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:22.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:22.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:22.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:22.885][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:22.886][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:22.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:22.895][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:22.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:22.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:22.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:22.901][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-03-20 19:34:22.903][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:22.906][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-03-20 19:34:22.907][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:22.909][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:22.910][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:22.912][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:22.913][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:22.914][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:22.918][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:22.919][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:22.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:22.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:22.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:22.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:22.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:22.933][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-03-20 19:34:22.937][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:22.938][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:22.940][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-03-20 19:34:23.277][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-03-20 19:34:23.617][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:23.621][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-03-20 19:34:23.626][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-03-20 19:34:23.631][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-03-20 19:34:23.633][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:23.636][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:23.637][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:23.640][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:23.641][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:23.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:23.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:23.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:23.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:23.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:23.659][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:23.661][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:23.662][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.664][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:23.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:23.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.671][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:23.673][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:23.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.675][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.691][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:23.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:23.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.699][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:23.700][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:23.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.703][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.705][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:23.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:23.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.710][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:23.711][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:23.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.713][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.715][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:23.717][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:23.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.719][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.721][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:23.723][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:23.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.725][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.727][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:23.729][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:23.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.731][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.733][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:23.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:23.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.740][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:23.741][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:23.743][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.744][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:23.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:23.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.752][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:23.754][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:23.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.756][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.758][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:23.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:23.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.765][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:23.766][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:23.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.769][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.771][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:23.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:23.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.776][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:23.778][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:23.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.780][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.782][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:23.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:23.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:23.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:23.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:23.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:23.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:23.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:23.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:23.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:23.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:23.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:23.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:23.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:23.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:23.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:23.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:23.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:23.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:23.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:23.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:23.833][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-03-20 19:34:23.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:23.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:23.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:23.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:23.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:23.841][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:23.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:23.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:23.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:23.846][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:23.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:23.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:23.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:23.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:23.859][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:23.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:23.862][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-03-20 19:34:23.863][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:23.865][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-03-20 19:34:23.867][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:23.868][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:23.870][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:23.871][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:23.873][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:23.874][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:23.877][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:23.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:23.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:23.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:23.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:23.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:23.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:23.890][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-03-20 19:34:23.894][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:23.895][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:23.897][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-03-20 19:34:24.237][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-03-20 19:34:26.359][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:26.362][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-03-20 19:34:26.366][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-03-20 19:34:26.369][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-03-20 19:34:26.371][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:26.373][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:26.374][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:26.376][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:26.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:26.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:26.384][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:26.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:26.386][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:26.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:26.389][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:26.390][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:26.391][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.392][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:26.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:26.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.398][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:26.400][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:26.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.401][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.409][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:26.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:26.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.420][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:26.421][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:26.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.423][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.424][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:26.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:26.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.429][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:26.430][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:26.431][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.432][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.434][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:26.435][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:26.436][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.437][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.438][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:26.439][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:26.440][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.441][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.443][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:26.444][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:26.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.446][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.448][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:26.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:26.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.453][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:26.454][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:26.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.456][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:26.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:26.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.462][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:26.464][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:26.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.466][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.468][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:26.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:26.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.471][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:26.472][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:26.473][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.474][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.476][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:26.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:26.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.481][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:26.482][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:26.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.484][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.485][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:26.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:26.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:26.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:26.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:26.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:26.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:26.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:26.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:26.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:26.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:26.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:26.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:26.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:26.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:26.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:26.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:26.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:26.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:26.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:26.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:26.539][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-03-20 19:34:26.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:26.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:26.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:26.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:26.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:26.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:26.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:26.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:26.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:26.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:26.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:26.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:26.562][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:26.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:26.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:26.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:26.566][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-03-20 19:34:26.567][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:26.569][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-03-20 19:34:26.570][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:26.571][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:26.572][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:26.573][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:26.574][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:26.575][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:26.577][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:26.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:26.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:26.585][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:26.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:26.587][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:26.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:26.589][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-03-20 19:34:26.592][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:26.592][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:26.594][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-03-20 19:34:26.936][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-03-20 19:34:27.281][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:27.284][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-03-20 19:34:27.287][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-03-20 19:34:27.291][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-03-20 19:34:27.293][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:27.294][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:27.295][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:27.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:27.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:27.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:27.305][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:27.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:27.307][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:27.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:27.310][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:27.311][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:27.312][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.314][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:27.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:27.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.319][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:27.320][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:27.321][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.322][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.330][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:27.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:27.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.343][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:27.344][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:27.345][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.346][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.347][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:27.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:27.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.351][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:27.353][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:27.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.354][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.355][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:27.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:27.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.359][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:27.360][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:27.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.362][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.363][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:27.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:27.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.368][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:27.369][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:27.371][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.372][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.373][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:27.375][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:27.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.377][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.378][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:27.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:27.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.382][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:27.383][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:27.384][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.385][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:27.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:27.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.391][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:27.392][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:27.393][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.394][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.396][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:27.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:27.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.399][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:27.400][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:27.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.402][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.404][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:27.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:27.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.408][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:27.409][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:27.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.411][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.412][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:27.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:27.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.416][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:27.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:27.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:27.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:27.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:27.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:27.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.427][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:27.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:27.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:27.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:27.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:27.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:27.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:27.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:27.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:27.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:27.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:27.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:27.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:27.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:27.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:27.463][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-03-20 19:34:27.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:27.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:27.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:27.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:27.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:27.472][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:27.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:27.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:27.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:27.477][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:27.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:27.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:27.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:27.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:27.488][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:27.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:27.491][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-03-20 19:34:27.492][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:27.494][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-03-20 19:34:27.495][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:27.497][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:27.498][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:27.500][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:27.501][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:27.502][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:27.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:27.508][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:27.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:27.516][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:27.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:27.518][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:27.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:27.520][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-03-20 19:34:27.523][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:27.524][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:27.526][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-03-20 19:34:27.867][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-03-20 19:34:28.213][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:28.215][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-03-20 19:34:28.220][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-03-20 19:34:28.224][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-03-20 19:34:28.227][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:28.229][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:28.231][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:28.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:28.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:28.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:28.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:28.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:28.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:28.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:28.260][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:28.262][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:28.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.264][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:28.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:28.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.272][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:28.273][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:28.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.275][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.276][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:28.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:28.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.281][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:28.283][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:28.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.285][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.287][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:28.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:28.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.293][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:28.294][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:28.295][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.296][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.297][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:28.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:28.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.302][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:28.303][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:28.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.305][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.307][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:28.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:28.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.312][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:28.313][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:28.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.315][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.316][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:28.318][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:28.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.320][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.322][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:28.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:28.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.326][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:28.327][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:28.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.330][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:28.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:28.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.337][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:28.338][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:28.340][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.341][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.343][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:28.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:28.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.347][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:28.348][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:28.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.350][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.352][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:28.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:28.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.357][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:28.359][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:28.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.361][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.363][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:28.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:28.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:28.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:28.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:28.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:28.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:28.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:28.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:28.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:28.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:28.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:28.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:28.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:28.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:28.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:28.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:28.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:28.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:28.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:28.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:28.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:28.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:28.427][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-03-20 19:34:28.428][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:28.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:28.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.433][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:28.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:28.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:28.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:28.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:28.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:28.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:28.444][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:28.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:28.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:28.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:28.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:28.456][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:28.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:28.459][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-03-20 19:34:28.460][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:28.462][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-03-20 19:34:28.464][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:28.465][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:28.467][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:28.468][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:28.469][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:28.470][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:28.474][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:28.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:28.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:28.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:28.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:28.490][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:28.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:28.494][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-03-20 19:34:28.498][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:28.500][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:28.502][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-03-20 19:34:28.840][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-03-20 19:34:29.185][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2025-03-20 19:34:29.187][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-03-20 19:34:29.189][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-03-20 19:34:29.193][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-03-20 19:34:29.196][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-03-20 19:34:29.198][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:29.211][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:29.213][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:29.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:29.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:29.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:29.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:29.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:29.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:29.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:29.230][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:29.231][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:29.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.233][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:29.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:29.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.238][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:29.239][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:29.240][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.242][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.243][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:29.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:29.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.248][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:29.249][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:29.250][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.251][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.252][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:29.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:29.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.258][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:29.259][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:29.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.261][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.263][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:29.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:29.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.268][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:29.269][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:29.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.272][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.273][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:29.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:29.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.277][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:29.278][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:29.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.281][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.282][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:29.283][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:29.285][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.285][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.287][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:29.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:29.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.290][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:29.292][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:29.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.294][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:29.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:29.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.300][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:29.301][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:29.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.303][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.305][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:29.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:29.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.311][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:29.312][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:29.313][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.314][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.316][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:29.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:29.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.322][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:29.323][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:29.331][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.333][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.335][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:29.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:29.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:29.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:29.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:29.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:29.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:29.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:29.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:29.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:29.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:29.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:29.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:29.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:29.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:29.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:29.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:29.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:29.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:29.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:29.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:29.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:29.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:29.395][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-03-20 19:34:29.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:29.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:29.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:29.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:29.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:29.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:29.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:29.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:29.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:29.414][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:29.415][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:29.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:29.425][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:29.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:29.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:29.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:29.431][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-03-20 19:34:29.433][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:29.436][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-03-20 19:34:29.437][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:29.439][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:29.441][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:29.442][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:29.444][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:29.445][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:29.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:29.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:29.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:29.460][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:29.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:29.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:29.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:29.467][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-03-20 19:34:29.470][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:29.480][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:29.482][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-03-20 19:34:29.825][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-03-20 19:34:30.171][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:30.174][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-03-20 19:34:30.179][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-03-20 19:34:30.182][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-03-20 19:34:30.184][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:30.185][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:30.187][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:30.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:30.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:30.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:30.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:30.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:30.202][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:30.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:30.206][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:30.208][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:30.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.211][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:30.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:30.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.220][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:30.221][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:30.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.224][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.226][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:30.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:30.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.231][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:30.233][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:30.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.235][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.237][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:30.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:30.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.242][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:30.243][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:30.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.245][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.247][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:30.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:30.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.252][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:30.253][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:30.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.255][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.257][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:30.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:30.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.261][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:30.263][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:30.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.266][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.267][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:30.268][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:30.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.270][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.271][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:30.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:30.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.276][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:30.278][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:30.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.280][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:30.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:30.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.286][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:30.287][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:30.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.289][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.299][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:30.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:30.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.306][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:30.307][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:30.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.309][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.312][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:30.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:30.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.316][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:30.317][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:30.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.320][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.322][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:30.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:30.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:30.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:30.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:30.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:30.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:30.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:30.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.338][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:30.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:30.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:30.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:30.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:30.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:30.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:30.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:30.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:30.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:30.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:30.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:30.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:30.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:30.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:30.369][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-03-20 19:34:30.370][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:30.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:30.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.376][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:30.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:30.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:30.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:30.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:30.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:30.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:30.384][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:30.385][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:30.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:30.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:30.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:30.397][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:30.399][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[2025-03-20 19:34:30.401][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-03-20 19:34:30.403][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:30.405][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-03-20 19:34:30.407][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:30.408][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:30.409][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:30.410][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:30.411][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:30.412][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:30.422][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:30.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:30.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:30.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:30.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:30.434][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:30.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:30.437][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-03-20 19:34:30.441][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:30.442][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:30.444][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-03-20 19:34:32.925][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-03-20 19:34:33.301][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2025-03-20 19:34:33.304][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-03-20 19:34:33.307][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-03-20 19:34:33.313][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-03-20 19:34:33.317][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-03-20 19:34:33.321][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:33.323][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:33.325][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:33.328][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:33.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:33.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:33.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:33.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:33.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:33.344][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.TRACE[2025-03-20 19:34:33.348][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:33.350][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:33.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.353][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:33.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:33.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.361][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:33.362][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:33.364][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.365][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.367][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:33.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:33.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.373][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:33.374][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:33.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.377][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.379][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:33.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:33.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.386][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:33.387][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:33.389][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.390][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.392][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:33.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:33.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.397][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:33.399][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:33.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.402][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.404][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:33.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:33.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.410][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:33.411][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:33.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.414][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.415][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:33.417][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:33.418][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.419][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.421][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:33.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:33.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.441][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:33.443][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:33.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.446][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:33.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:33.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.454][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:33.455][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:33.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.458][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:33.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:33.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.467][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:33.468][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:33.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.471][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.473][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:33.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:33.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.478][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:33.480][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:33.481][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.482][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.484][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:33.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:33.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:33.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:33.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:33.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:33.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:33.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:33.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:33.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:33.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:33.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:33.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:33.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:33.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:33.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:33.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:33.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:33.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:33.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:33.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:33.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:33.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:33.543][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-03-20 19:34:33.544][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:33.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:33.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:33.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:33.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:33.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:33.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:33.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:33.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:33.560][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:33.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:33.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:33.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:33.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:33.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:33.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:33.584][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-03-20 19:34:33.586][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:33.588][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-03-20 19:34:33.590][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:33.591][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:33.593][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:33.594][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:33.595][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:33.596][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:33.600][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:33.601][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:33.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:33.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:33.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:33.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:33.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:33.616][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-03-20 19:34:33.620][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:33.621][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:33.623][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-03-20 19:34:33.961][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-03-20 19:34:34.310][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:34.313][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-03-20 19:34:34.319][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-03-20 19:34:34.324][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-03-20 19:34:34.326][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:34.328][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:34.330][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:34.332][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:34.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:34.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:34.345][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:34.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:34.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:34.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:34.353][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:34.355][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:34.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.358][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:34.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:34.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.367][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:34.369][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:34.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.371][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.373][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:34.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:34.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.378][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:34.379][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:34.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.381][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.383][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:34.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:34.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.388][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:34.389][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:34.391][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.391][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.393][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:34.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:34.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.399][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:34.400][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:34.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.417][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.419][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:34.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:34.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.425][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:34.427][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:34.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.429][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.431][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:34.432][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:34.434][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.435][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.437][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:34.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:34.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.442][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:34.444][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:34.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.446][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:34.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:34.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.453][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:34.455][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:34.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.458][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:34.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:34.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.466][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:34.468][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:34.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.470][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.472][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:34.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:34.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.477][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:34.479][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:34.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.481][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.483][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:34.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:34.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:34.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:34.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:34.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:34.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:34.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:34.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:34.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:34.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:34.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:34.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:34.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:34.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:34.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:34.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:34.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:34.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:34.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:34.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:34.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:34.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:34.540][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-03-20 19:34:34.548][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:34.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:34.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.556][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:34.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:34.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:34.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:34.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:34.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:34.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:34.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:34.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:34.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:34.575][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:34.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:34.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:34.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:34.581][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-03-20 19:34:34.582][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:34.585][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-03-20 19:34:34.586][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:34.587][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:34.588][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:34.590][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:34.591][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:34.592][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:34.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:34.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:34.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:34.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:34.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:34.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:34.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:34.610][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-03-20 19:34:34.613][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:34.615][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:34.616][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-03-20 19:34:34.955][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-03-20 19:34:35.294][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:35.296][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-03-20 19:34:35.301][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-03-20 19:34:35.305][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-03-20 19:34:35.307][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:35.309][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:35.311][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:35.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:35.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:35.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:35.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:35.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:35.326][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:35.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:35.331][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:35.332][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:35.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.335][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:35.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:35.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.342][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:35.343][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:35.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.345][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.347][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:35.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:35.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.353][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:35.354][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:35.363][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.368][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.370][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:35.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:35.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.376][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:35.377][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:35.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.379][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:35.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:35.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.385][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:35.386][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:35.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.389][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.390][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:35.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:35.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.395][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:35.397][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:35.398][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.399][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.401][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:35.402][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:35.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.404][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.406][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:35.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:35.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.410][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:35.412][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:35.413][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.414][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.416][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:35.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:35.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.421][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:35.422][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:35.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.424][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.426][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:35.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:35.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.432][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:35.433][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:35.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.436][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.438][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:35.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:35.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.443][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:35.445][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:35.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.448][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.450][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:35.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:35.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:35.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:35.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:35.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:35.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:35.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:35.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:35.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:35.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:35.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:35.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:35.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:35.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:35.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:35.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:35.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:35.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:35.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:35.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:35.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:35.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:35.517][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-03-20 19:34:35.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:35.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:35.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.523][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:35.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:35.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:35.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:35.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:35.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:35.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:35.566][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 19:34:35.571][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:35.573][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:35.576][private$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[2025-03-20 19:34:38.053][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[2025-03-20 19:34:38.475][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:38.479][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-03-20 19:34:38.485][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-03-20 19:34:38.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:38.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:38.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:38.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:38.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:38.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:38.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:38.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.510][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:38.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:38.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:38.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:38.527][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:38.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:38.536][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:38.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:38.544][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.560][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:38.570][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:38.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:38.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:38.579][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:38.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:38.582][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:38.583][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.TRACE[2025-03-20 19:34:38.585][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.590][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.604][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:38.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:38.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:38.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:38.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:38.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:38.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:38.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:38.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.625][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.639][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:38.643][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:38.644][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:38.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:38.652][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:38.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:38.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:38.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:38.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:38.846][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:38.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:38.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:38.854][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:38.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:38.857][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:38.858][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.TRACE[2025-03-20 19:34:38.859][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.865][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:38.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:38.876][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:38.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:38.883][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:38.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:38.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:38.888][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.TRACE[2025-03-20 19:34:38.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.894][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:38.903][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:38.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:38.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:38.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:38.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:38.912][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:38.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:38.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.920][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.926][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:38.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:38.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:38.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:38.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:38.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:38.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:38.943][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[2025-03-20 19:34:38.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:38.958][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:38.958][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:38.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:38.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:38.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:38.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:38.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:38.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:38.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:38.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:38.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:38.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:38.988][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:38.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:38.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:38.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:38.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:38.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:39.001][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.013][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:39.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:39.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:39.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:39.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:39.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:39.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:39.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:39.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.038][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.044][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:39.050][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:39.051][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:39.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:39.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:39.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:39.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:39.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:39.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.071][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:39.081][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:39.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:39.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:39.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:39.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:39.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:39.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:39.099][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.105][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.111][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:39.117][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:39.118][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:39.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:39.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:39.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:39.131][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:39.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:39.134][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.141][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:39.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:39.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:39.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:39.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:39.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:39.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:39.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:39.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.176][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:39.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:39.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:39.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:39.202][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:39.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:39.205][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:39.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:39.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.223][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:39.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:39.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:39.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:39.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:39.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:39.245][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:39.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:39.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:39.269][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:39.270][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:39.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:39.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:39.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:39.284][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:39.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:39.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:39.309][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:39.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:39.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:39.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:39.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:39.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:39.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:39.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.335][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:39.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:39.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:39.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:39.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:39.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:39.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:39.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:39.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:39.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:39.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:39.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:39.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:39.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:39.435][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[2025-03-20 19:34:39.439][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:39.466][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:39.468][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-20 19:34:41.637][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-20 19:34:41.977][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:41.980][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-03-20 19:34:41.985][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-03-20 19:34:41.990][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 19:34:41.994][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:41.996][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:42.002][private$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[2025-03-20 19:34:42.381][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[2025-03-20 19:34:42.720][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:42.723][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-03-20 19:34:42.728][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-03-20 19:34:42.735][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:42.736][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:42.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:42.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:42.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:42.746][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:42.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:42.748][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-03-20 19:34:42.749][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:42.752][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-03-20 19:34:42.754][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:42.755][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:42.756][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:42.758][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:42.759][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:42.761][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:42.764][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:42.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:42.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:42.773][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:42.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:42.777][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:42.781][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[2025-03-20 19:34:42.783][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-03-20 19:34:42.787][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:42.789][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:42.791][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-03-20 19:34:43.135][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-03-20 19:34:43.491][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:43.494][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-03-20 19:34:43.498][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-03-20 19:34:43.502][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-03-20 19:34:43.504][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:43.510][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:43.512][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:43.514][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:43.515][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:43.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:43.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:43.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:43.527][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:43.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:43.536][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:43.538][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:43.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.540][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:43.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:43.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.547][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:43.548][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:43.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.551][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.552][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:43.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:43.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.557][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:43.559][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:43.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.562][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.563][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:43.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:43.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.569][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:43.570][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:43.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.573][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:43.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:43.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.582][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:43.584][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:43.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.586][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:43.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:43.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.594][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:43.595][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:43.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.600][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.604][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:43.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:43.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.610][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:43.612][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:43.613][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.614][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.616][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:43.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:43.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.622][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:43.623][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:43.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.625][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:43.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:43.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.632][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:43.634][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:43.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.636][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:43.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:43.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.642][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:43.643][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:43.644][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.645][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.646][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:43.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:43.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.652][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:43.657][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:43.658][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.660][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.661][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:43.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:43.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:43.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:43.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:43.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:43.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:43.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:43.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:43.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:43.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:43.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:43.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:43.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:43.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:43.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:43.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:43.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:43.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:43.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:43.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:43.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:43.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:43.720][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-03-20 19:34:43.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:43.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:43.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:43.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:43.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:43.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:43.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:43.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:43.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:43.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:43.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:43.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:43.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:43.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:43.765][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:43.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:43.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:43.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:43.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:43.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:43.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:43.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:43.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:43.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:43.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:43.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:43.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:43.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:43.792][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:43.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:43.795][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-03-20 19:34:43.796][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:43.799][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-03-20 19:34:43.801][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:43.803][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:43.804][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:43.806][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:43.807][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:43.809][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:43.812][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:43.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:43.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:43.823][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:43.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:43.826][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:43.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:43.829][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-03-20 19:34:43.850][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:43.851][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:43.854][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-03-20 19:34:44.192][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-03-20 19:34:44.529][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:44.532][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-03-20 19:34:44.536][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-03-20 19:34:44.539][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-03-20 19:34:44.542][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:44.543][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:44.544][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:44.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:44.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:44.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:44.554][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:44.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:44.556][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:44.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:44.560][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:44.561][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:44.562][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.563][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:44.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:44.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.570][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:44.572][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:44.573][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.574][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.575][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:44.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:44.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.580][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:44.581][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:44.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.584][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.585][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:44.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:44.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.590][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:44.591][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:44.592][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.594][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:44.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:44.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.600][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:44.601][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:44.603][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.604][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.605][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:44.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:44.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.609][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:44.611][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:44.612][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.613][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.615][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:44.616][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:44.617][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.618][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.619][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:44.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:44.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.623][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.624][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.625][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.626][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.628][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.633][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:44.634][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:44.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.636][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.637][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:44.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:44.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.640][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:44.642][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:44.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.644][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.645][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:44.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:44.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.649][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:44.650][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:44.651][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.653][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.654][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:44.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:44.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:44.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:44.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:44.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:44.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:44.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:44.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:44.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:44.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:44.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:44.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:44.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:44.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:44.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:44.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:44.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:44.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:44.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:44.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:44.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:44.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:44.712][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-03-20 19:34:44.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:44.761][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[2025-03-20 19:34:44.765][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:34:44.766][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-20 19:34:44.768][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:34:44.769][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-20 19:34:44.773][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:44.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:44.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:44.783][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:44.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:44.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:44.786][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.TRACE[2025-03-20 19:34:44.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:44.802][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:44.803][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:44.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:44.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:44.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:44.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:44.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:44.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.834][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:44.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:44.839][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:44.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:44.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:44.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:44.850][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:44.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:44.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:44.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:44.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:44.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:44.883][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:44.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:44.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:44.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:44.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.897][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.902][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:44.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:44.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:44.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:44.921][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:44.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:44.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:44.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:44.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:44.939][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:44.940][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:44.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:44.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:44.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:44.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:44.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:44.954][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:44.968][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:44.968][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:44.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:44.985][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:44.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:44.990][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:44.991][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.TRACE[2025-03-20 19:34:44.992][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:44.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:44.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:44.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:45.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.039][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.049][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.050][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.061][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.062][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.TRACE[2025-03-20 19:34:45.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.089][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:45.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.097][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.108][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.119][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.TRACE[2025-03-20 19:34:45.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.144][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.147][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[2025-03-20 19:34:45.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.152][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.161][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.170][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.173][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:45.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.180][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.201][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:45.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.214][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.218][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.227][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.229][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:45.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.236][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.246][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.247][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:45.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:45.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.312][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.329][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:45.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.350][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.370][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.373][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:45.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.389][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.400][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:45.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.407][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.444][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 19:34:45.447][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:34:45.449][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-20 19:34:45.451][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:34:45.453][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-20 19:34:45.457][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.470][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:45.473][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.484][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.495][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.508][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:45.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.515][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.534][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.542][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.544][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.545][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.TRACE[2025-03-20 19:34:45.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.570][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.580][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:45.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.623][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.626][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.627][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.TRACE[2025-03-20 19:34:45.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.655][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.664][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.665][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.677][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.TRACE[2025-03-20 19:34:45.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.683][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.692][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.693][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.701][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.704][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:45.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.712][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.733][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:45.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.749][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.757][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.759][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.761][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.TRACE[2025-03-20 19:34:45.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:45.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.813][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.815][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:45.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.844][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.845][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[2025-03-20 19:34:45.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:45.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.909][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.915][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:45.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.952][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.954][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:45.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:45.972][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:45.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:45.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:45.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:45.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:45.983][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:45.984][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.TRACE[2025-03-20 19:34:45.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:45.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:45.990][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:45.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:46.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:46.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:46.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:46.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:46.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:46.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:46.022][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:46.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:46.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:46.028][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:46.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:46.038][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:46.039][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:46.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:46.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:46.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:46.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:46.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:46.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:46.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:46.059][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:46.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:46.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:46.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:46.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:46.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:46.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:46.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:46.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:46.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:46.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:46.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:46.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:46.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:46.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:46.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:46.101][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:46.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:46.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:46.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:46.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:46.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:46.135][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-20 19:34:46.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-20 19:34:46.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-20 19:34:46.151][biodb::testThat]
biodb.INFO [2025-03-20 19:34:46.152][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-03-20 19:34:46.153][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:34:46.155][biodb::testThat]
biodb.TRACE[2025-03-20 19:34:46.158][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-20 19:34:46.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-20 19:34:46.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:46.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:46.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:46.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:46.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:46.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:46.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:46.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:46.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:46.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:46.178][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:46.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:46.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:46.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:46.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:46.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:46.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:46.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:46.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:46.199][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.DEBUG[2025-03-20 19:34:46.202][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[2025-03-20 19:34:46.206][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:46.208][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:46.210][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-20 19:34:46.555][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-20 19:34:46.894][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:46.897][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-03-20 19:34:46.901][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-03-20 19:34:46.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:46.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:46.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:46.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:46.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:46.915][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:46.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:46.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:46.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:46.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:46.921][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:46.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:46.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:46.926][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:46.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:46.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:46.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:46.931][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 19:34:46.934][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:46.935][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:46.938][private$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[2025-03-20 19:34:47.279][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[2025-03-20 19:34:47.623][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:47.626][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-03-20 19:34:47.633][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-03-20 19:34:47.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:47.639][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:47.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:47.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:47.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:47.652][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:47.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:47.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:47.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:47.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.661][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:47.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:47.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:47.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:47.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:47.673][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:47.674][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:47.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:47.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:47.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:47.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:47.687][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.TRACE[2025-03-20 19:34:47.689][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:47.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:47.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.694][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:47.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:47.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:47.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:47.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:47.705][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-20 19:34:47.707][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:47.708][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:47.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:47.718][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:47.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:47.720][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:47.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:47.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.733][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:47.735][private$selectFields]
biodb.TRACE[2025-03-20 19:34:47.736][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 19:34:47.737][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 19:34:47.738][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:47.739][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.741][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.743][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.745][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.746][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.751][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.752][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:47.754][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:47.755][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.757][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.760][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.760][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 19:34:47.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.791][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-20 19:34:47.793][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:47.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:47.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:47.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:47.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:47.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:47.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:47.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.820][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:47.821][private$selectFields]
biodb.TRACE[2025-03-20 19:34:47.822][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 19:34:47.823][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 19:34:47.825][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:47.826][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.827][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.829][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.830][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.831][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.832][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.849][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.850][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:47.852][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:47.853][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.855][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.857][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.858][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 19:34:47.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.874][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-20 19:34:47.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:47.876][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:47.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:47.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:47.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:47.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:47.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:47.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.900][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:47.901][private$selectFields]
biodb.TRACE[2025-03-20 19:34:47.902][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 19:34:47.903][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 19:34:47.904][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:47.906][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.907][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.909][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.911][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.912][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.913][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.915][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.916][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:47.917][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:47.918][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.919][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.920][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.921][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.922][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 19:34:47.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.929][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:47.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.939][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-20 19:34:47.940][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-20 19:34:47.941][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-20 19:34:47.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:47.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:47.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:47.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:47.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.965][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:47.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:47.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:47.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:47.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:47.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:47.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:48.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:48.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:48.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:48.063][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:48.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:48.066][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:48.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:48.070][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[2025-03-20 19:34:48.074][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:48.076][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:48.078][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-20 19:34:48.425][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-20 19:34:48.773][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:48.776][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-03-20 19:34:48.781][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-03-20 19:34:48.787][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 19:34:48.791][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:48.792][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:48.794][private$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[2025-03-20 19:34:49.139][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[2025-03-20 19:34:49.483][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:49.486][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-03-20 19:34:49.492][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-03-20 19:34:49.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:49.498][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:49.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:49.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:49.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:49.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:49.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:49.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:49.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:49.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:49.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:49.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:49.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:49.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:49.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:49.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:49.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:49.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:49.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:49.542][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:49.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:49.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:49.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:49.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.551][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:49.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:49.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:49.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:49.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:49.561][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:49.562][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:49.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:49.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:49.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:49.572][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:49.573][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.TRACE[2025-03-20 19:34:49.575][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:49.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:49.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:49.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:49.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.585][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:49.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:49.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:49.622][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-20 19:34:49.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:49.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:49.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:49.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:49.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:49.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:49.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:49.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.692][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:49.692][private$selectFields]
biodb.TRACE[2025-03-20 19:34:49.693][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 19:34:49.694][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 19:34:49.696][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:49.696][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.697][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.700][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.701][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.702][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.704][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.705][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:49.705][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:49.707][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.708][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.710][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.712][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 19:34:49.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.728][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-20 19:34:49.729][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:49.730][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:49.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:49.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:49.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:49.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:49.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:49.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.762][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.795][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:49.796][private$selectFields]
biodb.TRACE[2025-03-20 19:34:49.797][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 19:34:49.798][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 19:34:49.799][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:49.801][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.802][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.805][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.806][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.807][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.809][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.811][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:49.825][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:49.827][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.828][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.829][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.830][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.831][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 19:34:49.833][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.849][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-20 19:34:49.850][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:49.851][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:49.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:49.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:49.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:49.863][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:49.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:49.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.877][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:49.878][private$selectFields]
biodb.TRACE[2025-03-20 19:34:49.879][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 19:34:49.881][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 19:34:49.882][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:49.883][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.885][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.887][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.889][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.890][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.893][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.894][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:49.896][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:49.897][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.898][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.899][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.900][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.902][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 19:34:49.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:49.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.919][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-20 19:34:49.920][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-20 19:34:49.921][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-20 19:34:49.934][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-20 19:34:49.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-20 19:34:49.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-20 19:34:49.946][biodb::testThat]
biodb.INFO [2025-03-20 19:34:49.947][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-03-20 19:34:49.948][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:34:49.949][biodb::testThat]
biodb.TRACE[2025-03-20 19:34:49.953][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-20 19:34:49.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-20 19:34:49.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.958][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:49.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:49.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.963][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:49.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:49.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:49.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:49.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:49.975][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:49.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:49.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:49.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:49.983][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:49.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:49.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:49.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:49.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:49.995][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:49.996][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[2025-03-20 19:34:49.999][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[2025-03-20 19:34:50.003][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:34:50.005][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-20 19:34:50.007][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:34:50.009][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-20 19:34:50.012][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:50.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:50.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:50.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:50.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:50.029][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:50.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:50.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.038][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.042][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:50.048][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[2025-03-20 19:34:50.052][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:34:50.054][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-20 19:34:50.057][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:34:50.059][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-20 19:34:50.062][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:50.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:50.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:50.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:50.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:50.076][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:50.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:50.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:50.092][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:50.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:50.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:50.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:50.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:50.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:50.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:50.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.114][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:50.119][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-20 19:34:50.121][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:50.122][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:50.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:50.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:50.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:50.139][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:50.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:50.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.177][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.178][private$selectFields]
biodb.TRACE[2025-03-20 19:34:50.179][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 19:34:50.180][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 19:34:50.181][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.183][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.184][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.187][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.188][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.190][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.191][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.193][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.204][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.205][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.206][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.208][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.210][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 19:34:50.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.225][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-20 19:34:50.226][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:50.227][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:50.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:50.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:50.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:50.237][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:50.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:50.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.247][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.248][private$selectFields]
biodb.TRACE[2025-03-20 19:34:50.249][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 19:34:50.249][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 19:34:50.250][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.251][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.252][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.253][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.254][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.255][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.255][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.256][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.257][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.258][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.259][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.260][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.261][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.262][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.263][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 19:34:50.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.275][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-20 19:34:50.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:50.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:50.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:50.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:50.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:50.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:50.288][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.TRACE[2025-03-20 19:34:50.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.324][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.325][private$selectFields]
biodb.TRACE[2025-03-20 19:34:50.327][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 19:34:50.328][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 19:34:50.329][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.330][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.332][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.334][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.335][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.336][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.339][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.340][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.355][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.357][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.359][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.361][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.363][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 19:34:50.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.380][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-20 19:34:50.382][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-20 19:34:50.383][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-20 19:34:50.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:50.422][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:50.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:50.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:50.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:50.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:50.434][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:50.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:50.439][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[2025-03-20 19:34:50.443][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:34:50.444][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-20 19:34:50.446][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:34:50.448][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-20 19:34:50.451][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[2025-03-20 19:34:50.454][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:34:50.456][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-20 19:34:50.458][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:34:50.460][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-20 19:34:50.463][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:50.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:50.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:50.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:50.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:50.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:50.476][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.TRACE[2025-03-20 19:34:50.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:50.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:50.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:50.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:50.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:50.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:50.504][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:50.506][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.TRACE[2025-03-20 19:34:50.507][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:50.523][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:50.523][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:50.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:50.531][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:50.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:50.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:50.533][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.TRACE[2025-03-20 19:34:50.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.552][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:50.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:50.558][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-20 19:34:50.560][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:50.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:50.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:50.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:50.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:50.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:50.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:50.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.608][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.609][private$selectFields]
biodb.TRACE[2025-03-20 19:34:50.610][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 19:34:50.611][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 19:34:50.612][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.613][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.614][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.616][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.617][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.618][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.620][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.622][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.635][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.636][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.638][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.639][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.640][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.641][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 19:34:50.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.645][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.655][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-20 19:34:50.656][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:50.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:50.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:50.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:50.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:50.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:50.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:50.670][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.679][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.681][private$selectFields]
biodb.TRACE[2025-03-20 19:34:50.682][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 19:34:50.683][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 19:34:50.684][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.686][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.687][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.689][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.690][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.691][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.694][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.695][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.696][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.697][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.698][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.701][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.702][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 19:34:50.703][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.714][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.719][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-20 19:34:50.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:50.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:50.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:50.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:50.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:50.732][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:50.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:50.734][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.773][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.774][private$selectFields]
biodb.TRACE[2025-03-20 19:34:50.775][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 19:34:50.777][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 19:34:50.778][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.779][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.781][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.784][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.785][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.786][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.789][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.790][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.804][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:50.805][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.806][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.809][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.810][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 19:34:50.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:50.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.827][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-20 19:34:50.828][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-20 19:34:50.830][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-20 19:34:50.843][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-20 19:34:50.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-20 19:34:50.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-20 19:34:50.856][biodb::testThat]
biodb.INFO [2025-03-20 19:34:50.858][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-03-20 19:34:50.860][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:34:50.861][biodb::testThat]
biodb.TRACE[2025-03-20 19:34:50.865][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-20 19:34:50.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-20 19:34:50.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.876][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.886][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:50.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:50.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:50.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:50.905][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:50.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:50.906][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:50.907][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[2025-03-20 19:34:50.911][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[2025-03-20 19:34:50.915][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:34:50.917][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-20 19:34:50.919][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:34:50.920][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-20 19:34:50.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:50.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:50.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:50.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:50.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:50.932][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:50.933][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[2025-03-20 19:34:50.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.938][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.941][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:50.945][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[2025-03-20 19:34:50.948][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:34:50.949][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-20 19:34:50.950][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:34:50.952][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-20 19:34:50.954][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:50.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:50.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:50.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:50.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:50.965][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:50.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:50.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.978][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:50.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:50.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:50.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:50.989][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:50.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:50.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:50.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:50.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:51.001][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:51.002][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.TRACE[2025-03-20 19:34:51.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:51.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:51.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:51.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:51.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:51.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:51.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:51.016][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-20 19:34:51.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:51.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:51.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:51.025][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:51.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:51.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:51.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:51.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.039][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.040][private$selectFields]
biodb.TRACE[2025-03-20 19:34:51.041][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 19:34:51.041][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 19:34:51.042][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.043][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.044][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.046][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.046][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.047][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.049][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.050][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.051][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.052][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.053][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.055][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.057][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 19:34:51.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.063][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.070][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-20 19:34:51.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:51.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:51.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:51.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:51.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:51.083][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:51.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:51.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.090][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.094][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.095][private$selectFields]
biodb.TRACE[2025-03-20 19:34:51.096][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 19:34:51.097][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 19:34:51.098][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.099][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.100][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.103][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.104][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.106][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.108][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.109][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.110][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.111][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.112][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.115][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.116][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 19:34:51.117][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.128][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.134][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-20 19:34:51.136][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:51.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:51.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:51.144][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:51.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:51.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:51.147][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[2025-03-20 19:34:51.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.158][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.158][private$selectFields]
biodb.TRACE[2025-03-20 19:34:51.159][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 19:34:51.160][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 19:34:51.161][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.162][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.163][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.164][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.165][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.166][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.168][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.169][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.170][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.171][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.172][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.174][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.175][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 19:34:51.176][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.190][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-20 19:34:51.191][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-20 19:34:51.191][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-20 19:34:51.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.230][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:51.243][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:51.245][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:51.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:51.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:51.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:51.255][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:51.256][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[2025-03-20 19:34:51.258][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[2025-03-20 19:34:51.261][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:34:51.263][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-20 19:34:51.264][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:34:51.265][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-20 19:34:51.268][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[2025-03-20 19:34:51.271][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:34:51.273][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-20 19:34:51.274][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:34:51.275][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-20 19:34:51.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:51.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:51.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:51.287][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:51.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:51.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:51.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:51.291][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:51.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:51.305][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:51.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:51.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:51.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:51.316][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:51.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:51.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:51.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:51.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:51.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:51.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:51.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:51.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:51.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:51.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:51.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:51.388][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-20 19:34:51.389][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:51.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:51.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:51.399][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:51.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:51.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:51.403][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[2025-03-20 19:34:51.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.415][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.417][private$selectFields]
biodb.TRACE[2025-03-20 19:34:51.418][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 19:34:51.419][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 19:34:51.420][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.421][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.429][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.433][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.434][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.436][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.438][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.439][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.440][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.441][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.442][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.445][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.446][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 19:34:51.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.460][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-20 19:34:51.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:51.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:51.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:51.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:51.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:51.472][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:51.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:51.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.482][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.483][private$selectFields]
biodb.TRACE[2025-03-20 19:34:51.484][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 19:34:51.485][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 19:34:51.486][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.487][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.488][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.489][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.490][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.494][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.496][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.497][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.498][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.499][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.500][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.501][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.503][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.505][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 19:34:51.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.518][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-20 19:34:51.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:51.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:51.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:51.531][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:51.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:51.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:51.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:51.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.548][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.549][private$selectFields]
biodb.TRACE[2025-03-20 19:34:51.550][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 19:34:51.550][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 19:34:51.551][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.553][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.554][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.555][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.555][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.556][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.557][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.559][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.560][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.561][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 19:34:51.562][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.563][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.565][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.566][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 19:34:51.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.572][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:51.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:51.581][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-20 19:34:51.582][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-20 19:34:51.584][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-20 19:34:51.613][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-20 19:34:51.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-20 19:34:51.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:51.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-20 19:34:51.623][biodb::testThat]
biodb.INFO [2025-03-20 19:34:51.624][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-03-20 19:34:51.626][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:34:51.627][biodb::testThat]
biodb.DEBUG[2025-03-20 19:34:51.629][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-03-20 19:34:51.631][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:34:51.633][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-03-20 19:34:51.634][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:34:51.636][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:51.637][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:51.638][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:51.639][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:51.640][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:51.643][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:51.644][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:51.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:51.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:51.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:51.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:51.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:51.658][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-03-20 19:34:51.661][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:51.662][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:51.664][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-03-20 19:34:52.006][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-03-20 19:34:52.347][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:52.350][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-03-20 19:34:52.354][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-03-20 19:34:52.358][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-03-20 19:34:52.361][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:52.362][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:34:52.364][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:52.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:52.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:52.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:52.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:52.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:52.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:52.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:52.383][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:52.384][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:52.386][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.387][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:52.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:52.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:52.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:52.394][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:52.395][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:52.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.398][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:52.399][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:52.401][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:52.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.403][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:52.411][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:52.413][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:52.414][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.416][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:52.418][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:52.420][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:52.421][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.423][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:52.425][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:52.427][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:52.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.431][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:52.433][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:52.434][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:52.436][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.437][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:52.439][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:52.440][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:52.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.443][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:52.445][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:52.446][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:52.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.449][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:52.450][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:52.452][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:52.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.454][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:52.456][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:52.458][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:52.459][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.460][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:52.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:52.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:52.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:52.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:52.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:52.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:52.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:52.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:52.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:52.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:52.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:52.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:52.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:52.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:52.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:52.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:52.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:52.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:52.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:52.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:52.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:52.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:52.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:52.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:52.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:52.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:52.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:52.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:52.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:52.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:52.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:52.526][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-03-20 19:34:52.527][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-03-20 19:34:52.540][biodb::testThat]
biodb.INFO [2025-03-20 19:34:52.541][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-03-20 19:34:52.543][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:34:52.544][biodb::testThat]
biodb.DEBUG[2025-03-20 19:34:52.556][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-03-20 19:34:52.558][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-03-20 19:34:52.560][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-03-20 19:34:52.562][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-03-20 19:34:52.567][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-03-20 19:34:52.569][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:34:52.570][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:34:52.571][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:52.573][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:34:52.574][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:34:52.580][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:52.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:52.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:52.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:52.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:52.596][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:52.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:52.609][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-03-20 19:34:52.612][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:52.614][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:52.615][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-03-20 19:34:52.954][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-03-20 19:34:53.298][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:53.301][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-03-20 19:34:53.305][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-03-20 19:34:53.307][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:53.308][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:53.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:53.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:53.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:53.320][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:53.322][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[2025-03-20 19:34:53.323][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-03-20 19:34:53.327][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:53.328][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:53.330][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-03-20 19:34:53.667][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-03-20 19:34:55.705][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:55.708][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-03-20 19:34:55.714][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-03-20 19:34:55.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:55.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:55.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:55.728][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:55.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:55.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:55.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:55.733][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-03-20 19:34:55.736][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:55.737][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:55.739][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-03-20 19:34:56.078][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-03-20 19:34:56.421][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:56.425][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-03-20 19:34:56.430][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-03-20 19:34:56.434][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-03-20 19:34:56.438][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:34:56.440][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-03-20 19:34:56.442][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-03-20 19:34:56.444][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:56.446][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:56.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:56.455][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:56.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:56.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:56.460][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.TRACE[2025-03-20 19:34:56.463][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.464][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.465][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.467][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.474][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:56.475][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:56.476][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.477][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.478][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:56.480][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:56.481][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.483][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.484][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:56.485][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:56.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.487][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.489][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:56.490][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:56.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.491][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.493][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:56.493][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:56.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.495][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.496][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:56.497][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:56.498][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.499][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.501][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:56.502][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:56.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.504][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.506][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:56.507][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:56.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.510][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.511][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:56.512][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:56.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.513][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.515][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:56.516][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:56.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.518][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:56.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:56.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:56.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:56.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:56.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:56.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:56.549][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:56.550][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:56.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:56.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:56.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:56.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:56.562][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.TRACE[2025-03-20 19:34:56.564][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.565][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.566][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.567][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.574][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:56.576][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:56.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.578][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.579][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:56.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:56.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.583][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:56.584][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:56.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.586][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.587][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:56.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:56.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.592][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:56.593][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:56.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.595][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.596][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:56.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:56.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.601][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:56.602][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:56.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.605][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.606][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:56.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:56.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.611][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:56.612][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:56.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.614][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.616][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:56.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:56.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.620][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:56.621][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:56.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.623][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.624][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:56.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:56.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.629][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:56.630][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:56.631][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.632][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:56.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:56.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.637][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:56.639][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:56.639][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.640][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.641][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:56.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:56.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.647][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:56.649][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:56.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.651][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.653][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:56.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:56.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.658][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:56.659][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:56.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.661][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.663][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:56.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:56.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:56.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:56.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:56.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:56.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:56.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:56.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:56.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:34:56.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:56.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:56.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:56.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:56.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:56.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:34:56.732][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.733][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.736][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.742][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:56.744][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:56.745][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.746][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.747][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:34:56.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:34:56.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.753][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:56.755][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:56.756][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.757][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.759][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:34:56.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:34:56.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.788][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:56.790][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:56.792][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.793][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.794][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:34:56.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:34:56.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.801][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:56.802][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:56.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.805][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.806][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:34:56.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:34:56.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.813][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:56.815][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:56.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.817][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.820][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:56.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:34:56.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.847][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:56.849][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:56.850][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.851][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.852][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:34:56.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:34:56.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.857][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:56.858][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:56.860][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.861][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:56.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:56.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.866][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:56.867][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:56.868][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.869][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.870][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:56.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:56.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.875][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:56.876][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:56.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.879][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.880][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:34:56.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:34:56.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.885][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:56.886][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:56.887][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.888][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.889][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:34:56.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:34:56.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:56.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:56.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.899][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:56.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:56.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:34:56.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:34:56.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:56.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:34:56.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:34:56.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:56.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:34:56.970][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-03-20 19:34:56.971][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-03-20 19:34:56.972][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-03-20 19:34:56.996][biodb::testThat]
biodb.INFO [2025-03-20 19:34:56.998][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-03-20 19:34:56.999][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:34:57.000][biodb::testThat]
biodb.INFO [2025-03-20 19:34:57.033][biodb::testThat]
biodb.INFO [2025-03-20 19:34:57.035][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-03-20 19:34:57.036][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:34:57.037][biodb::testThat]
biodb.INFO [2025-03-20 19:34:57.051][biodb::testThat]
biodb.INFO [2025-03-20 19:34:57.052][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-03-20 19:34:57.054][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:34:57.055][biodb::testThat]
biodb.DEBUG[2025-03-20 19:34:57.059][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[2025-03-20 19:34:57.063][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:57.064][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:57.067][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-03-20 19:34:57.433][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-03-20 19:34:57.904][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:34:57.906][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-03-20 19:34:57.913][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-03-20 19:34:57.936][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:34:57.938][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:34:57.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:57.940][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:34:57.941][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:57.942][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:34:57.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:34:57.948][ef$get] fields variable is a list.
biodb.INFO [2025-03-20 19:34:57.951][biodb::testThat]
biodb.INFO [2025-03-20 19:34:57.952][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2025-03-20 19:34:57.953][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:34:57.954][biodb::testThat]
biodb.ERROR[2025-03-20 19:34:57.973][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-03-20 19:34:57.996][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-03-20 19:34:58.020][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-20 19:34:58.022][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-20 19:34:58.024][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-20 19:34:58.025][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-20 19:34:58.026][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:58.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:58.028][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:58.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:58.030][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-20 19:34:58.046][biodb::testContext]
biodb.INFO [2025-03-20 19:34:58.047][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 19:34:58.048][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-03-20 19:34:58.049][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 19:34:58.051][biodb::testContext]
biodb.INFO [2025-03-20 19:34:58.054][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-20 19:34:58.056][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-20 19:34:58.061][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 19:34:58.063][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-20 19:34:58.064][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-20 19:34:58.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.068][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-20 19:34:58.071][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-20 19:34:58.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.076][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-20 19:34:58.077][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-20 19:34:58.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.082][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-20 19:34:58.083][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-20 19:34:58.085][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-20 19:34:58.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.091][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-20 19:34:58.092][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-20 19:34:58.094][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-20 19:34:58.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.099][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-20 19:34:58.101][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-20 19:34:58.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.106][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-20 19:34:58.107][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-20 19:34:58.109][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-20 19:34:58.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.113][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-20 19:34:58.114][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-20 19:34:58.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.119][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-20 19:34:58.120][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-20 19:34:58.122][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-20 19:34:58.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.126][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-20 19:34:58.127][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-20 19:34:58.128][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-20 19:34:58.129][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-20 19:34:58.131][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-20 19:34:58.132][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-20 19:34:58.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.136][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-20 19:34:58.137][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-20 19:34:58.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.145][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-20 19:34:58.146][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-20 19:34:58.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.151][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-20 19:34:58.153][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-20 19:34:58.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.170][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-20 19:34:58.171][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-20 19:34:58.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.175][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-20 19:34:58.176][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-20 19:34:58.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.179][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[2025-03-20 19:34:58.180][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-20 19:34:58.182][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-20 19:34:58.499][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-20 19:34:58.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.504][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-20 19:34:58.505][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-20 19:34:58.506][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-20 19:34:58.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.513][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-20 19:34:58.516][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 19:34:58.517][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-20 19:34:58.518][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 19:34:58.520][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 19:34:58.521][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 19:34:58.523][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 19:34:58.524][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 19:34:58.525][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 19:34:58.527][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 19:34:58.529][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 19:34:58.531][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 19:34:58.534][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-20 19:34:58.535][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 19:34:58.537][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:34:58.538][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 19:34:58.539][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 19:34:58.539][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 19:34:58.539][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 19:34:58.539][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 19:34:58.539][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 19:34:58.541][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 19:34:58.542][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:34:58.543][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:34:58.545][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 19:34:58.546][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:34:58.547][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:34:58.549][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 19:34:58.550][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:34:58.551][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 19:34:58.552][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 19:34:58.554][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 19:34:58.555][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:34:58.557][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-20 19:34:58.558][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 19:34:58.559][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 19:34:58.560][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 19:34:58.561][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 19:34:58.563][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 19:34:58.564][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 19:34:58.565][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 19:34:58.566][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 19:34:58.567][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 19:34:58.568][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 19:34:58.569][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 19:34:58.570][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-20 19:34:58.571][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 19:34:58.572][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:34:58.573][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 19:34:58.577][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 19:34:58.577][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 19:34:58.577][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 19:34:58.577][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 19:34:58.577][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 19:34:58.579][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 19:34:58.580][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:34:58.582][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:34:58.583][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 19:34:58.584][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:34:58.586][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:34:58.587][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 19:34:58.588][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:34:58.590][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 19:34:58.592][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 19:34:58.595][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 19:34:58.599][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:34:58.601][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-20 19:34:58.603][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 19:34:58.605][self$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[2025-03-20 19:34:58.606][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 19:34:58.608][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 19:34:58.609][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 19:34:58.610][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 19:34:58.611][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 19:34:58.612][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 19:34:58.613][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 19:34:58.614][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 19:34:58.616][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 19:34:58.617][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-20 19:34:58.618][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 19:34:58.619][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:34:58.620][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 19:34:58.621][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:34:58.622][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 19:34:58.623][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:34:58.624][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:34:58.625][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 19:34:58.626][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:34:58.628][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:34:58.629][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 19:34:58.630][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:34:58.632][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 19:34:58.633][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 19:34:58.635][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 19:34:58.636][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:34:58.637][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-20 19:34:58.639][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 19:34:58.641][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 19:34:58.642][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 19:34:58.648][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 19:34:58.649][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 19:34:58.651][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 19:34:58.652][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 19:34:58.653][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 19:34:58.655][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 19:34:58.656][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 19:34:58.657][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 19:34:58.659][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-20 19:34:58.660][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 19:34:58.661][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:34:58.664][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 19:34:58.666][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:34:58.670][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 19:34:58.671][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:34:58.673][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:34:58.674][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 19:34:58.676][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:34:58.677][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:34:58.679][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 19:34:58.680][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:34:58.681][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 19:34:58.683][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 19:34:58.684][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 19:34:58.686][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:34:58.687][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 19:34:58.689][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:58.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:58.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:58.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:58.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:58.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:58.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:58.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:58.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.714][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[2025-03-20 19:34:58.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:58.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:58.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:58.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:58.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:58.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:58.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:58.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:58.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.749][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[2025-03-20 19:34:58.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:58.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:58.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:58.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:58.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:58.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:58.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:58.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:58.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.774][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[2025-03-20 19:34:58.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:58.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:58.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.779][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[2025-03-20 19:34:58.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:58.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:58.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.785][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[2025-03-20 19:34:58.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:58.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:58.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:58.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:58.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:58.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:58.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:58.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:58.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:58.807][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[2025-03-20 19:34:58.809][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-20 19:34:58.812][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-20 19:34:58.815][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-20 19:34:58.817][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-20 19:34:58.819][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 19:34:58.821][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-20 19:34:58.823][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-20 19:34:58.825][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-20 19:34:58.827][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-20 19:34:58.829][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-20 19:34:58.831][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 19:34:58.833][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-20 19:34:58.835][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-20 19:34:58.837][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-20 19:34:58.839][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-20 19:34:58.841][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-20 19:34:58.843][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-20 19:34:58.845][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-20 19:34:58.847][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 19:34:58.848][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-20 19:34:58.850][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-20 19:34:58.852][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-20 19:34:58.854][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-20 19:34:58.856][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-20 19:34:58.858][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-20 19:34:58.864][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-20 19:34:58.867][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-20 19:34:58.869][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-20 19:34:58.871][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-20 19:34:58.873][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-20 19:34:58.876][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-20 19:34:58.877][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-20 19:34:58.880][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-20 19:34:58.883][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-20 19:34:58.888][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-20 19:34:58.889][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-20 19:34:58.891][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-20 19:34:58.894][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-20 19:34:58.896][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-20 19:34:58.898][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-20 19:34:58.900][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-20 19:34:58.902][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-20 19:34:58.904][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-20 19:34:58.906][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-20 19:34:58.908][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-20 19:34:58.910][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-20 19:34:58.912][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-20 19:34:58.914][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-20 19:34:58.917][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-20 19:34:58.919][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-20 19:34:58.921][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-20 19:34:58.924][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-20 19:34:58.926][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-20 19:34:58.929][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-20 19:34:58.931][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-20 19:34:58.933][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-20 19:34:58.937][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-20 19:34:58.940][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-20 19:34:58.942][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-20 19:34:58.944][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-20 19:34:58.946][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-20 19:34:58.948][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-20 19:34:58.952][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-20 19:34:58.954][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-20 19:34:58.959][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-20 19:34:58.961][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-20 19:34:58.964][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 19:34:58.965][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 19:34:58.967][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-20 19:34:58.970][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-20 19:34:58.972][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-20 19:34:58.974][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-20 19:34:58.976][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-20 19:34:58.978][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-20 19:34:58.980][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-20 19:34:58.982][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-20 19:34:58.984][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-20 19:34:58.986][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-20 19:34:58.988][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-20 19:34:58.990][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-20 19:34:58.992][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-20 19:34:58.994][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-20 19:34:58.996][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-20 19:34:59.006][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-20 19:34:59.013][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-20 19:34:59.015][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 19:34:59.017][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:59.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:59.019][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:59.021][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[2025-03-20 19:34:59.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:59.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:59.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:59.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:59.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:59.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:59.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:59.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:59.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:59.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:59.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:59.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:59.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:59.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:59.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:59.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:59.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:59.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:59.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:59.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:59.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:59.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:59.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:59.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:59.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:59.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:59.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:59.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:59.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:59.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:59.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:59.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:59.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:59.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:59.066][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[2025-03-20 19:34:59.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:59.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:59.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:59.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:59.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:59.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:59.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:59.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:59.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:59.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:59.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:59.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:59.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:59.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:59.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:59.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:59.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:59.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:59.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:59.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:59.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:59.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:59.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:59.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:59.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:59.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:59.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:59.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:59.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:59.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:59.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:59.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:59.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:59.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:59.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:59.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:59.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:59.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:59.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:59.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:59.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:59.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:59.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:59.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:59.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:59.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:59.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:59.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:59.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:59.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:59.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:59.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:59.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:59.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:59.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:59.145][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[2025-03-20 19:34:59.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:59.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:59.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:59.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:59.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:59.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:59.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:59.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:59.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:59.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:59.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:59.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:59.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:59.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:59.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:59.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:59.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:59.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:59.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:59.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:59.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:59.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:34:59.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:34:59.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:34:59.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:34:59.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:34:59.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:34:59.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:34:59.184][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-20 19:34:59.197][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-20 19:34:59.201][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 19:34:59.203][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-20 19:34:59.204][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 19:34:59.206][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 19:34:59.207][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 19:34:59.209][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 19:34:59.210][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-20 19:34:59.212][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-20 19:34:59.213][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-20 19:34:59.215][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 19:34:59.216][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 19:34:59.218][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-20 19:34:59.219][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 19:34:59.221][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-20 19:34:59.221][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-20 19:34:59.221][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-20 19:34:59.221][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-20 19:34:59.221][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-20 19:34:59.221][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-20 19:34:59.221][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-20 19:34:59.221][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-20 19:34:59.221][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-20 19:34:59.221][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-20 19:34:59.221][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-20 19:34:59.223][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-20 19:34:59.224][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 19:34:59.224][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 19:34:59.224][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 19:34:59.225][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-20 19:34:59.227][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:34:59.228][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:34:59.230][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 19:34:59.231][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:34:59.234][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:34:59.236][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 19:34:59.238][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:34:59.238][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-20 19:34:59.239][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 19:34:59.240][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 19:34:59.242][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-20 19:34:59.243][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-20 19:34:59.243][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-20 19:34:59.245][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 19:34:59.248][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 19:34:59.250][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-20 19:34:59.252][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 19:34:59.255][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 19:34:59.258][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 19:34:59.263][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-20 19:34:59.265][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-20 19:34:59.266][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-20 19:34:59.268][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-20 19:34:59.270][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 19:34:59.272][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 19:34:59.273][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-20 19:34:59.275][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-20 19:34:59.277][biodb::testThat]
biodb.INFO [2025-03-20 19:34:59.279][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2025-03-20 19:34:59.280][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:34:59.282][biodb::testThat]
biodb.DEBUG[2025-03-20 19:34:59.287][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-20 19:34:59.292][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:34:59.294][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:34:59.296][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-03-20 19:34:59.628][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-03-20 19:35:00.125][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:35:00.128][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-03-20 19:35:00.134][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-03-20 19:35:00.141][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[2025-03-20 19:35:00.146][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:35:00.148][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:35:00.151][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-20 19:35:00.492][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-20 19:35:00.954][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:35:00.957][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-03-20 19:35:00.963][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-03-20 19:35:00.966][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:35:00.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:00.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:00.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:00.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:00.979][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:00.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:00.983][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-20 19:35:00.989][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:35:00.990][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:35:00.993][private$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[2025-03-20 19:35:01.339][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[2025-03-20 19:35:01.702][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:35:01.705][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-03-20 19:35:01.710][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-03-20 19:35:01.714][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:35:01.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:01.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:01.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:01.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:01.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:01.729][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[2025-03-20 19:35:01.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:35:01.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:01.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:01.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:01.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:01.767][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:01.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:01.776][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[2025-03-20 19:35:01.780][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:35:01.783][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-20 19:35:01.785][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:35:01.787][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-20 19:35:01.790][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:35:01.791][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:01.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:01.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:01.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:01.806][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:01.807][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[2025-03-20 19:35:01.809][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[2025-03-20 19:35:01.814][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:35:01.816][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-20 19:35:01.818][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:35:01.820][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-20 19:35:01.822][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:35:01.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:01.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:01.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:01.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:01.837][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:01.838][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[2025-03-20 19:35:01.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:35:01.841][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:01.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:01.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:01.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:01.853][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:01.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:01.865][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[2025-03-20 19:35:01.870][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:35:01.878][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-20 19:35:01.932][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:35:01.938][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-20 19:35:01.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:35:01.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:01.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:01.969][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:01.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:01.973][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:01.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:01.986][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[2025-03-20 19:35:01.992][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:35:02.016][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-20 19:35:02.029][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:35:02.032][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-20 19:35:02.035][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:35:02.037][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:02.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:02.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:02.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:02.065][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:02.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:02.070][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[2025-03-20 19:35:02.082][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:35:02.084][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:35:02.087][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-20 19:35:02.454][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-20 19:35:02.794][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:35:02.797][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-03-20 19:35:02.803][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-03-20 19:35:02.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:35:02.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:02.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:02.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:02.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:02.820][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:02.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-20 19:35:02.832][biodb::testThat]
biodb.INFO [2025-03-20 19:35:02.833][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2025-03-20 19:35:02.835][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:35:02.836][biodb::testThat]
biodb.DEBUG[2025-03-20 19:35:02.841][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-20 19:35:02.845][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:35:02.847][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:35:02.850][private$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[2025-03-20 19:35:03.192][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[2025-03-20 19:35:05.712][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:35:05.715][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-03-20 19:35:05.722][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-03-20 19:35:05.726][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:35:05.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:05.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:05.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:05.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:05.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:05.742][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[2025-03-20 19:35:05.748][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[2025-03-20 19:35:05.753][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:35:05.755][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:35:05.758][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-20 19:35:06.104][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-20 19:35:06.447][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:35:06.451][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-03-20 19:35:06.457][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-03-20 19:35:06.460][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:35:06.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:06.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:06.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:06.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:06.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:06.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-20 19:35:06.485][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-20 19:35:06.487][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-20 19:35:06.489][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-20 19:35:06.491][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-20 19:35:06.493][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:06.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:06.496][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:06.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:06.499][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:06.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-20 19:35:06.507][biodb::testContext]
biodb.INFO [2025-03-20 19:35:06.508][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 19:35:06.510][biodb::testContext] Test context - Test web services
biodb.INFO [2025-03-20 19:35:06.512][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 19:35:06.513][biodb::testContext]
biodb.INFO [2025-03-20 19:35:06.516][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-20 19:35:06.519][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-20 19:35:06.525][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 19:35:06.526][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-20 19:35:06.528][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-20 19:35:06.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:06.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:06.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:06.533][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-20 19:35:06.535][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-20 19:35:06.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:06.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:06.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:06.540][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-20 19:35:06.541][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-20 19:35:06.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:06.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:06.544][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[2025-03-20 19:35:06.546][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-20 19:35:06.547][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-20 19:35:06.548][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-20 19:35:06.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:06.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:06.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:06.553][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-20 19:35:06.555][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-20 19:35:06.556][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-20 19:35:06.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:06.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:06.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:06.561][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-20 19:35:06.562][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-20 19:35:06.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:06.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:06.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:06.567][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-20 19:35:06.569][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-20 19:35:06.570][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-20 19:35:06.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:06.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:06.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:06.575][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-20 19:35:06.577][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-20 19:35:06.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:06.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:06.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:06.581][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-20 19:35:06.583][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-20 19:35:06.584][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-20 19:35:06.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:06.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:06.588][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[2025-03-20 19:35:06.589][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-20 19:35:06.590][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-20 19:35:06.592][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-20 19:35:06.593][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-20 19:35:06.594][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-20 19:35:06.596][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-20 19:35:06.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:06.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:06.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:06.601][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-20 19:35:06.602][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-20 19:35:06.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:06.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:06.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:06.607][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-20 19:35:06.609][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-20 19:35:06.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:06.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:06.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:06.613][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-20 19:35:06.615][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-20 19:35:06.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:06.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:06.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:06.619][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-20 19:35:06.621][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-20 19:35:06.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:06.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:06.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:06.625][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-20 19:35:06.627][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-20 19:35:06.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:06.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:06.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:06.632][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-20 19:35:06.633][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-20 19:35:06.672][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-20 19:35:06.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:06.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:06.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:06.678][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-20 19:35:06.679][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-20 19:35:06.681][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-20 19:35:06.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:06.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:06.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:06.686][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-20 19:35:06.688][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:06.690][self$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[2025-03-20 19:35:06.692][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:06.693][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 19:35:06.695][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:06.696][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 19:35:06.697][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:06.699][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 19:35:06.700][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 19:35:06.701][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 19:35:06.703][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:06.704][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-20 19:35:06.706][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 19:35:06.707][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:06.708][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:06.710][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 19:35:06.710][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 19:35:06.710][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 19:35:06.710][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 19:35:06.710][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 19:35:06.711][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 19:35:06.713][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:35:06.714][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:35:06.715][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 19:35:06.717][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:35:06.718][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:35:06.719][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 19:35:06.720][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:06.721][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 19:35:06.731][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 19:35:06.733][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:06.734][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:06.736][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-20 19:35:06.739][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:06.740][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 19:35:06.747][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:06.749][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 19:35:06.750][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:06.752][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 19:35:06.753][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:06.754][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 19:35:06.756][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 19:35:06.764][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 19:35:06.766][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:06.767][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-20 19:35:06.769][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 19:35:06.770][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:06.772][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:06.778][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 19:35:06.778][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 19:35:06.778][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 19:35:06.778][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 19:35:06.778][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 19:35:06.779][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 19:35:06.781][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:35:06.782][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:35:06.783][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 19:35:06.785][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:35:06.786][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:35:06.788][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 19:35:06.797][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:06.798][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 19:35:06.800][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 19:35:06.801][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:06.803][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:06.804][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-20 19:35:06.813][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:06.815][self$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[2025-03-20 19:35:06.816][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:06.818][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 19:35:06.819][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:06.820][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 19:35:06.829][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:06.831][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 19:35:06.833][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 19:35:06.834][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 19:35:06.836][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:06.837][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-20 19:35:06.845][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 19:35:06.847][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:06.849][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:06.850][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:06.852][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 19:35:06.853][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:35:06.859][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:35:06.861][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 19:35:06.863][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:35:06.864][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:35:06.865][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 19:35:06.867][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:06.868][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 19:35:06.875][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 19:35:06.876][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:06.878][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:06.880][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-20 19:35:06.882][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:06.884][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 19:35:06.893][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:06.895][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 19:35:06.897][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:06.898][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 19:35:06.916][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:06.944][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 19:35:06.945][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 19:35:06.947][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 19:35:06.949][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:06.961][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-20 19:35:06.962][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 19:35:06.964][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:06.965][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:06.966][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:06.968][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 19:35:06.969][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:35:06.977][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:35:06.978][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 19:35:06.980][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:35:06.981][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:35:06.983][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 19:35:06.984][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:06.985][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 19:35:06.993][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 19:35:06.995][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:06.997][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:06.999][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 19:35:07.000][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.047][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[2025-03-20 19:35:07.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.060][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[2025-03-20 19:35:07.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.126][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[2025-03-20 19:35:07.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.194][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-20 19:35:07.196][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-20 19:35:07.205][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-20 19:35:07.208][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-20 19:35:07.210][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 19:35:07.212][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-20 19:35:07.220][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-20 19:35:07.222][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-20 19:35:07.225][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-20 19:35:07.227][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-20 19:35:07.238][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 19:35:07.241][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-20 19:35:07.245][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-20 19:35:07.247][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-20 19:35:07.255][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-20 19:35:07.257][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-20 19:35:07.259][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-20 19:35:07.262][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-20 19:35:07.273][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 19:35:07.278][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-20 19:35:07.280][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-20 19:35:07.282][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-20 19:35:07.289][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-20 19:35:07.292][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-20 19:35:07.294][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-20 19:35:07.297][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-20 19:35:07.307][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-20 19:35:07.311][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-20 19:35:07.313][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-20 19:35:07.316][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-20 19:35:07.327][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-20 19:35:07.329][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-20 19:35:07.331][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-20 19:35:07.333][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-20 19:35:07.335][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-20 19:35:07.343][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-20 19:35:07.346][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-20 19:35:07.348][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-20 19:35:07.350][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-20 19:35:07.362][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-20 19:35:07.365][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-20 19:35:07.367][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-20 19:35:07.369][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-20 19:35:07.380][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-20 19:35:07.382][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-20 19:35:07.385][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-20 19:35:07.387][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-20 19:35:07.397][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-20 19:35:07.400][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-20 19:35:07.403][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-20 19:35:07.405][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-20 19:35:07.413][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-20 19:35:07.415][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-20 19:35:07.417][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-20 19:35:07.420][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-20 19:35:07.430][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-20 19:35:07.432][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-20 19:35:07.435][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-20 19:35:07.437][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-20 19:35:07.447][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-20 19:35:07.450][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-20 19:35:07.452][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-20 19:35:07.455][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-20 19:35:07.463][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-20 19:35:07.468][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-20 19:35:07.472][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-20 19:35:07.482][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 19:35:07.485][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 19:35:07.488][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-20 19:35:07.490][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-20 19:35:07.500][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-20 19:35:07.503][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-20 19:35:07.506][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-20 19:35:07.509][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-20 19:35:07.519][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-20 19:35:07.522][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-20 19:35:07.525][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-20 19:35:07.527][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-20 19:35:07.537][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-20 19:35:07.540][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-20 19:35:07.543][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-20 19:35:07.552][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-20 19:35:07.555][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-20 19:35:07.557][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-20 19:35:07.560][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-20 19:35:07.569][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 19:35:07.571][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.575][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:07.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:07.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.604][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[2025-03-20 19:35:07.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:07.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:07.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.624][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[2025-03-20 19:35:07.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:07.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:07.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:07.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:07.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:07.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:07.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:07.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:07.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:07.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:07.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.729][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[2025-03-20 19:35:07.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:07.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:07.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:07.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:07.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.774][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[2025-03-20 19:35:07.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:07.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:07.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:07.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:07.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:07.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:07.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.829][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[2025-03-20 19:35:07.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:07.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:07.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:07.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:07.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:07.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:07.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:07.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:07.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:07.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:07.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:07.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:07.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:07.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:07.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:07.938][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-20 19:35:07.940][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-20 19:35:07.949][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:07.951][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-20 19:35:07.953][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:07.955][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 19:35:07.957][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:07.958][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 19:35:07.970][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:07.972][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-20 19:35:07.974][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-20 19:35:07.976][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 19:35:07.983][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:07.985][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-20 19:35:07.987][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 19:35:07.989][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-20 19:35:07.989][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-20 19:35:07.989][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-20 19:35:07.989][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-20 19:35:07.989][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-20 19:35:07.989][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-20 19:35:07.989][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-20 19:35:07.989][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-20 19:35:07.989][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-20 19:35:07.989][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-20 19:35:07.989][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-20 19:35:07.992][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:07.999][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 19:35:07.999][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 19:35:07.999][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 19:35:08.002][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-20 19:35:08.011][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:35:08.013][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:35:08.015][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 19:35:08.017][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:35:08.018][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:35:08.020][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 19:35:08.022][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:35:08.022][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-20 19:35:08.024][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 19:35:08.032][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 19:35:08.034][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:08.036][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-20 19:35:08.036][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-20 19:35:08.038][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 19:35:08.046][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 19:35:08.049][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-20 19:35:08.051][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 19:35:08.054][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 19:35:08.062][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 19:35:08.068][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-20 19:35:08.069][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-20 19:35:08.078][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-20 19:35:08.082][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-20 19:35:08.084][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 19:35:08.086][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 19:35:08.094][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-20 19:35:08.097][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-20 19:35:08.099][biodb::testThat]
biodb.INFO [2025-03-20 19:35:08.101][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-03-20 19:35:08.103][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:35:08.111][biodb::testThat]
biodb.DEBUG[2025-03-20 19:35:08.117][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-20 19:35:08.129][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:35:08.132][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-20 19:35:08.135][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:35:08.145][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-20 19:35:08.151][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-20 19:35:08.162][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:35:08.164][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:35:08.167][private$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[2025-03-20 19:35:09.665][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[2025-03-20 19:35:10.006][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:35:10.010][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-03-20 19:35:10.016][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-03-20 19:35:10.031][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-20 19:35:10.033][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-20 19:35:10.035][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-20 19:35:10.036][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-20 19:35:10.038][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:10.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:10.040][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:10.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:10.043][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.044][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.INFO [2025-03-20 19:35:10.049][biodb::testContext]
biodb.INFO [2025-03-20 19:35:10.051][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 19:35:10.052][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-03-20 19:35:10.054][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 19:35:10.055][biodb::testContext]
biodb.INFO [2025-03-20 19:35:10.058][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-20 19:35:10.061][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-20 19:35:10.067][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 19:35:10.068][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-20 19:35:10.070][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-20 19:35:10.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.075][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-20 19:35:10.077][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-20 19:35:10.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.082][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-20 19:35:10.083][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-20 19:35:10.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.088][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-20 19:35:10.090][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-20 19:35:10.091][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-20 19:35:10.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.096][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-20 19:35:10.097][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-20 19:35:10.099][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-20 19:35:10.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.104][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-20 19:35:10.105][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-20 19:35:10.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.110][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-20 19:35:10.111][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-20 19:35:10.113][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-20 19:35:10.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.118][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-20 19:35:10.119][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-20 19:35:10.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.124][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-20 19:35:10.125][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-20 19:35:10.127][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-20 19:35:10.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.131][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-20 19:35:10.133][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-20 19:35:10.134][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-20 19:35:10.136][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-20 19:35:10.137][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-20 19:35:10.138][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-20 19:35:10.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.142][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.DEBUG[2025-03-20 19:35:10.143][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-20 19:35:10.145][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-20 19:35:10.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.161][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-20 19:35:10.163][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-20 19:35:10.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.166][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[2025-03-20 19:35:10.173][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-20 19:35:10.175][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-20 19:35:10.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.180][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-20 19:35:10.187][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-20 19:35:10.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.193][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-20 19:35:10.195][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-20 19:35:10.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.204][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-20 19:35:10.206][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-20 19:35:10.292][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-20 19:35:10.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.296][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[2025-03-20 19:35:10.297][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-20 19:35:10.299][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-20 19:35:10.300][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-20 19:35:10.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.305][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-20 19:35:10.308][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:10.309][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-20 19:35:10.310][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:10.312][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 19:35:10.313][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:10.314][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 19:35:10.316][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:10.317][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 19:35:10.318][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 19:35:10.320][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 19:35:10.321][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:10.329][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-20 19:35:10.331][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 19:35:10.332][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:10.334][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:10.335][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 19:35:10.335][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 19:35:10.335][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 19:35:10.335][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 19:35:10.335][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 19:35:10.337][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 19:35:10.343][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:35:10.344][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:35:10.346][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 19:35:10.347][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:35:10.348][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:35:10.349][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 19:35:10.351][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:10.361][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 19:35:10.362][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 19:35:10.364][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:10.365][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:10.367][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-20 19:35:10.369][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:10.374][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 19:35:10.375][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:10.377][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 19:35:10.378][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:10.380][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 19:35:10.381][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:10.382][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 19:35:10.388][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 19:35:10.389][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 19:35:10.391][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:10.392][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-20 19:35:10.393][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 19:35:10.395][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:10.396][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:10.406][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 19:35:10.406][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 19:35:10.406][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 19:35:10.406][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 19:35:10.406][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 19:35:10.408][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 19:35:10.410][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:35:10.411][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:35:10.412][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 19:35:10.414][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:35:10.415][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:35:10.421][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 19:35:10.423][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:10.424][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 19:35:10.426][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 19:35:10.427][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:10.428][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:10.430][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-20 19:35:10.438][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:10.440][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-20 19:35:10.441][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:10.443][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 19:35:10.444][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:10.446][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 19:35:10.455][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:10.457][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 19:35:10.458][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 19:35:10.460][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 19:35:10.462][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:10.464][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-20 19:35:10.471][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 19:35:10.472][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:10.475][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:10.476][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:10.478][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 19:35:10.479][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:35:10.480][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:35:10.489][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 19:35:10.491][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:35:10.492][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:35:10.493][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 19:35:10.494][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:10.495][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 19:35:10.496][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 19:35:10.497][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:10.498][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:10.506][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-20 19:35:10.509][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:10.511][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 19:35:10.512][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:10.514][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 19:35:10.523][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:10.525][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 19:35:10.527][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:10.528][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 19:35:10.530][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 19:35:10.531][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 19:35:10.542][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:10.544][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-20 19:35:10.545][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 19:35:10.547][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:10.548][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:10.550][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:10.555][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 19:35:10.557][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:35:10.559][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:35:10.561][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 19:35:10.562][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:35:10.563][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:35:10.565][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 19:35:10.574][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:10.575][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 19:35:10.577][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 19:35:10.579][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:10.580][self$setPropertyValue]
biodb.DEBUG[2025-03-20 19:35:10.582][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 19:35:10.590][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:10.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:10.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:10.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:10.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:10.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:10.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:10.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:10.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:10.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:10.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:10.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:10.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:10.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:10.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.698][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.DEBUG[2025-03-20 19:35:10.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:10.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:10.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:10.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:10.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.728][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[2025-03-20 19:35:10.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:10.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:10.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:10.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:10.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:10.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:10.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.759][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[2025-03-20 19:35:10.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:10.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:10.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:10.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:10.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.784][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[2025-03-20 19:35:10.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:10.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:10.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.797][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[2025-03-20 19:35:10.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:10.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:10.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:10.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:10.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:10.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:10.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:10.822][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[2025-03-20 19:35:10.823][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-20 19:35:10.836][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-20 19:35:10.838][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-20 19:35:10.840][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-20 19:35:10.842][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 19:35:10.856][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-20 19:35:10.859][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-20 19:35:10.861][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-20 19:35:10.863][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-20 19:35:10.872][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-20 19:35:10.874][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 19:35:10.877][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-20 19:35:10.879][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-20 19:35:10.884][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-20 19:35:10.887][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-20 19:35:10.889][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-20 19:35:10.891][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-20 19:35:10.893][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-20 19:35:10.905][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 19:35:10.907][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-20 19:35:10.923][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-20 19:35:10.925][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-20 19:35:10.928][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-20 19:35:10.930][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-20 19:35:10.932][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-20 19:35:10.934][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-20 19:35:10.937][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-20 19:35:10.940][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-20 19:35:10.955][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-20 19:35:10.957][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-20 19:35:10.959][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-20 19:35:10.962][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-20 19:35:10.964][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-20 19:35:10.966][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-20 19:35:10.968][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-20 19:35:10.970][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-20 19:35:10.972][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-20 19:35:10.980][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-20 19:35:10.983][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-20 19:35:10.985][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-20 19:35:10.988][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-20 19:35:10.998][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-20 19:35:11.000][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-20 19:35:11.003][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-20 19:35:11.005][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-20 19:35:11.014][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-20 19:35:11.017][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-20 19:35:11.019][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-20 19:35:11.021][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-20 19:35:11.023][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-20 19:35:11.033][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-20 19:35:11.036][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-20 19:35:11.038][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-20 19:35:11.041][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-20 19:35:11.046][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-20 19:35:11.048][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-20 19:35:11.051][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-20 19:35:11.053][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-20 19:35:11.064][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-20 19:35:11.067][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-20 19:35:11.069][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-20 19:35:11.071][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-20 19:35:11.080][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-20 19:35:11.084][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-20 19:35:11.086][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-20 19:35:11.089][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-20 19:35:11.100][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 19:35:11.105][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 19:35:11.108][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-20 19:35:11.110][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-20 19:35:11.119][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-20 19:35:11.122][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-20 19:35:11.125][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-20 19:35:11.127][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-20 19:35:11.138][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-20 19:35:11.141][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-20 19:35:11.143][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-20 19:35:11.153][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-20 19:35:11.156][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-20 19:35:11.158][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-20 19:35:11.160][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-20 19:35:11.163][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-20 19:35:11.172][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-20 19:35:11.174][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-20 19:35:11.177][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-20 19:35:11.179][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 19:35:11.187][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:11.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:11.190][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:11.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:11.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:11.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:11.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:11.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:11.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:11.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:11.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:11.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:11.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:11.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:11.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:11.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:11.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:11.226][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.DEBUG[2025-03-20 19:35:11.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:11.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:11.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:11.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:11.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:11.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:11.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:11.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:11.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:11.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:11.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:11.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:11.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:11.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:11.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:11.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:11.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:11.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:11.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:11.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:11.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:11.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:11.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:11.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:11.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:11.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:11.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:11.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:11.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:11.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:11.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:11.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:11.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:11.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:11.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:11.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:11.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:11.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:11.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:11.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:11.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:11.322][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[2025-03-20 19:35:11.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:11.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:11.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:11.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:11.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:11.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:11.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:11.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:11.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:11.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:11.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:11.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:11.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:11.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:11.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:11.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:11.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:11.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:11.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:11.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:11.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:11.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:11.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:11.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:11.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:11.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:11.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:11.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:11.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:11.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:11.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:11.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:11.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:11.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:11.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:11.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:11.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:11.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:11.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:11.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:11.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:11.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:11.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:11.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:11.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:11.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:11.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:11.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:11.441][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[2025-03-20 19:35:11.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:11.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:11.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:11.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:11.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:11.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:11.460][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[2025-03-20 19:35:11.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 19:35:11.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:11.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:11.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:11.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:11.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:11.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 19:35:11.487][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-20 19:35:11.491][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-20 19:35:11.494][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:11.496][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-20 19:35:11.497][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:11.499][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 19:35:11.505][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:11.506][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 19:35:11.508][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:11.509][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-20 19:35:11.511][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-20 19:35:11.512][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 19:35:11.522][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:11.525][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-20 19:35:11.527][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 19:35:11.528][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-20 19:35:11.528][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-20 19:35:11.528][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-20 19:35:11.528][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-20 19:35:11.528][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-20 19:35:11.528][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-20 19:35:11.528][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-20 19:35:11.528][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-20 19:35:11.528][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-20 19:35:11.528][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-20 19:35:11.528][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-20 19:35:11.530][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-20 19:35:11.532][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 19:35:11.532][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 19:35:11.532][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 19:35:11.533][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-20 19:35:11.539][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:35:11.541][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:35:11.543][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 19:35:11.544][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 19:35:11.546][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 19:35:11.547][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 19:35:11.548][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:35:11.548][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-20 19:35:11.559][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 19:35:11.560][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 19:35:11.562][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-20 19:35:11.563][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-20 19:35:11.563][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-20 19:35:11.565][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 19:35:11.584][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 19:35:11.593][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-20 19:35:11.595][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 19:35:11.598][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 19:35:11.600][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 19:35:11.613][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-20 19:35:11.615][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-20 19:35:11.617][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-20 19:35:11.628][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-20 19:35:11.630][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 19:35:11.632][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 19:35:11.634][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-20 19:35:11.635][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-20 19:35:11.643][biodb::testThat]
biodb.INFO [2025-03-20 19:35:11.644][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-03-20 19:35:11.647][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 19:35:11.649][biodb::testThat]
biodb.DEBUG[2025-03-20 19:35:11.662][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-20 19:35:11.667][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:35:11.669][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-20 19:35:11.671][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:35:11.680][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-20 19:35:11.685][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[2025-03-20 19:35:11.696][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 19:35:11.698][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-03-20 19:35:11.700][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 19:35:11.702][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-03-20 19:35:11.719][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-03-20 19:35:11.721][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 19:35:11.724][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-03-20 19:35:11.732][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 19:35:11.734][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 19:35:11.735][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 19:35:11.737][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 19:35:11.739][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 19:35:11.749][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 19:35:11.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:35:11.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:11.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:11.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:11.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:11.783][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:11.785][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[2025-03-20 19:35:11.786][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-03-20 19:35:11.793][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 19:35:11.795][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 19:35:11.797][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-03-20 19:35:12.148][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-03-20 19:35:13.187][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 19:35:13.190][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-03-20 19:35:13.197][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-03-20 19:35:13.201][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-03-20 19:35:13.205][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 19:35:13.207][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 19:35:13.209][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 19:35:13.211][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 19:35:13.212][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:13.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:13.222][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:13.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:13.224][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:13.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 19:35:13.231][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:35:13.233][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:35:13.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.236][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:35:13.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:35:13.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.243][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:35:13.244][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:35:13.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.247][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.249][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 19:35:13.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 19:35:13.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.255][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:35:13.256][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:35:13.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.259][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.260][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 19:35:13.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 19:35:13.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.266][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 19:35:13.267][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 19:35:13.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.270][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.272][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 19:35:13.273][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 19:35:13.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.276][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.277][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:35:13.279][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:35:13.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.281][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.283][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:35:13.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 19:35:13.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.289][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:35:13.290][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:35:13.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.293][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.295][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 19:35:13.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 19:35:13.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.301][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:35:13.302][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:35:13.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.305][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.307][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:35:13.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 19:35:13.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.313][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:35:13.314][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:35:13.316][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.317][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.320][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 19:35:13.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 19:35:13.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.326][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:35:13.327][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:35:13.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.330][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.333][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 19:35:13.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 19:35:13.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.338][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:35:13.340][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:35:13.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.343][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.345][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 19:35:13.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 19:35:13.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:35:13.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:35:13.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:35:13.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:35:13.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:35:13.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:35:13.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 19:35:13.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 19:35:13.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:35:13.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:35:13.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:35:13.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:35:13.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:35:13.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:35:13.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:35:13.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:35:13.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:35:13.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:35:13.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 19:35:13.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 19:35:13.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 19:35:13.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 19:35:13.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 19:35:13.510][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-03-20 19:35:13.518][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-20 19:35:13.521][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-20 19:35:13.523][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-20 19:35:13.525][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-20 19:35:13.532][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 19:35:13.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 19:35:13.543][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 19:35:13.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 19:35:13.547][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 19:35:13.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
>
> proc.time()
user system elapsed
22.686 1.420 82.051
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 2.565 | 1.014 | 4.556 | |
| ChebiEntry | 0.341 | 0.015 | 0.376 | |