Pierrick Roger
| Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_21 |
| git_last_commit: b8d718f |
| git_last_commit_date: 2025-04-15 12:39:10 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-22 13:15 -0400 (Tue, 22 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 206/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.14.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| 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: 1.14.0 |
| 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_1.14.0.tar.gz |
| StartedAt: 2025-04-21 19:21:08 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 19:23:59 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 170.6 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* 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 ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ChebiConn 2.648 1.079 7.972
* 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 ‘1.14.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
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 [2025-04-21 19:22:13.010][biodb::testContext]
biodb.INFO [2025-04-21 19:22:13.015][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-21 19:22:13.017][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-04-21 19:22:13.018][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-21 19:22:13.020][biodb::testContext]
biodb.INFO [2025-04-21 19:22:13.028][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-21 19:22:13.031][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-21 19:22:13.041][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 19:22:13.042][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-21 19:22:13.044][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-21 19:22:13.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.050][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-21 19:22:13.078][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-21 19:22:13.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.084][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-21 19:22:13.086][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-21 19:22:13.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.091][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-21 19:22:13.092][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-21 19:22:13.094][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-21 19:22:13.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.097][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.DEBUG[2025-04-21 19:22:13.099][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-21 19:22:13.100][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-21 19:22:13.102][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-21 19:22:13.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.107][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-21 19:22:13.109][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-21 19:22:13.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.112][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[2025-04-21 19:22:13.114][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-21 19:22:13.115][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-21 19:22:13.117][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-21 19:22:13.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.122][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-21 19:22:13.123][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-21 19:22:13.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.127][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.DEBUG[2025-04-21 19:22:13.128][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-21 19:22:13.129][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-21 19:22:13.130][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-21 19:22:13.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.135][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-21 19:22:13.137][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-21 19:22:13.138][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-21 19:22:13.140][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-21 19:22:13.141][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-21 19:22:13.143][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-21 19:22:13.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.148][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-21 19:22:13.149][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-21 19:22:13.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.154][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-21 19:22:13.156][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-21 19:22:13.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.161][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-21 19:22:13.162][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-21 19:22:13.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.167][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-21 19:22:13.168][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-21 19:22:13.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.173][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-21 19:22:13.174][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-21 19:22:13.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.179][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-21 19:22:13.180][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-21 19:22:13.221][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-21 19:22:13.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.226][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.DEBUG[2025-04-21 19:22:13.227][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-21 19:22:13.229][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-21 19:22:13.230][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-21 19:22:13.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.239][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-21 19:22:13.283][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 19:22:13.317][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-21 19:22:13.319][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 19:22:13.320][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 19:22:13.322][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 19:22:13.323][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 19:22:13.325][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 19:22:13.326][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 19:22:13.328][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-21 19:22:13.329][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 19:22:13.330][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 19:22:13.335][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-21 19:22:13.337][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 19:22:13.338][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:22:13.341][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 19:22:13.342][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 19:22:13.342][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 19:22:13.342][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 19:22:13.342][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-21 19:22:13.342][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-21 19:22:13.344][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 19:22:13.345][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:22:13.346][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:22:13.348][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 19:22:13.349][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:22:13.350][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:22:13.351][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 19:22:13.353][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:22:13.354][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 19:22:13.355][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 19:22:13.357][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 19:22:13.358][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:22:13.360][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-21 19:22:13.362][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 19:22:13.363][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-21 19:22:13.365][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 19:22:13.366][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 19:22:13.367][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 19:22:13.368][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 19:22:13.370][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 19:22:13.371][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 19:22:13.372][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-21 19:22:13.373][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 19:22:13.375][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 19:22:13.376][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-21 19:22:13.377][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 19:22:13.379][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:22:13.380][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 19:22:13.381][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 19:22:13.381][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 19:22:13.381][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 19:22:13.381][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-21 19:22:13.381][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-21 19:22:13.383][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 19:22:13.384][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:22:13.385][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:22:13.386][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 19:22:13.387][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:22:13.389][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:22:13.390][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 19:22:13.391][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:22:13.392][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 19:22:13.393][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 19:22:13.395][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 19:22:13.396][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:22:13.397][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-21 19:22:13.399][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-21 19:22:13.405][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-21 19:22:13.425][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 19:22:13.427][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 19:22:13.431][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 19:22:13.445][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 19:22:13.447][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 19:22:13.448][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 19:22:13.450][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-21 19:22:13.455][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 19:22:13.460][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-21 19:22:13.466][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-21 19:22:13.468][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 19:22:13.470][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:22:13.471][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 19:22:13.473][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:22:13.474][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 19:22:13.475][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:22:13.477][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:22:13.478][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 19:22:13.480][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:22:13.481][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:22:13.483][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 19:22:13.484][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:22:13.486][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 19:22:13.487][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 19:22:13.488][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 19:22:13.490][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:22:13.492][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-21 19:22:13.494][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-21 19:22:13.496][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-21 19:22:13.498][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 19:22:13.499][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 19:22:13.501][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 19:22:13.502][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 19:22:13.503][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 19:22:13.505][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 19:22:13.506][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-21 19:22:13.508][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 19:22:13.510][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-21 19:22:13.511][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-21 19:22:13.512][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 19:22:13.514][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:22:13.515][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 19:22:13.517][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:22:13.518][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 19:22:13.519][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:22:13.521][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:22:13.522][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 19:22:13.524][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:22:13.525][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:22:13.527][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 19:22:13.528][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:22:13.529][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 19:22:13.531][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 19:22:13.532][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 19:22:13.534][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:22:13.539][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 19:22:13.540][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.542][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.DEBUG[2025-04-21 19:22:13.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.548][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[2025-04-21 19:22:13.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.554][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[2025-04-21 19:22:13.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.559][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[2025-04-21 19:22:13.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.565][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[2025-04-21 19:22:13.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.606][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[2025-04-21 19:22:13.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.612][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[2025-04-21 19:22:13.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.624][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[2025-04-21 19:22:13.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.651][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[2025-04-21 19:22:13.653][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-21 19:22:13.658][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-21 19:22:13.661][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-21 19:22:13.663][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-21 19:22:13.665][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-21 19:22:13.667][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-21 19:22:13.669][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-21 19:22:13.671][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-21 19:22:13.673][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-21 19:22:13.674][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-21 19:22:13.677][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-21 19:22:13.679][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-21 19:22:13.681][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-21 19:22:13.682][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-21 19:22:13.684][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-21 19:22:13.686][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-21 19:22:13.688][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-21 19:22:13.689][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-21 19:22:13.691][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-21 19:22:13.693][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-21 19:22:13.695][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-21 19:22:13.697][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-21 19:22:13.699][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-21 19:22:13.700][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-21 19:22:13.702][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-21 19:22:13.704][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-21 19:22:13.706][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-21 19:22:13.708][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-21 19:22:13.711][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-21 19:22:13.714][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-21 19:22:13.720][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-21 19:22:13.722][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-21 19:22:13.724][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-21 19:22:13.726][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-21 19:22:13.728][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-21 19:22:13.730][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-21 19:22:13.732][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-21 19:22:13.734][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-21 19:22:13.736][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-21 19:22:13.738][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-21 19:22:13.740][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-21 19:22:13.742][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-21 19:22:13.744][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-21 19:22:13.746][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-21 19:22:13.748][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-21 19:22:13.749][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-21 19:22:13.751][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-21 19:22:13.753][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-21 19:22:13.755][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-21 19:22:13.757][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-21 19:22:13.759][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-21 19:22:13.761][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-21 19:22:13.763][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-21 19:22:13.765][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-21 19:22:13.767][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-21 19:22:13.769][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-21 19:22:13.771][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-21 19:22:13.773][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-21 19:22:13.775][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-21 19:22:13.777][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-21 19:22:13.779][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-21 19:22:13.781][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-21 19:22:13.783][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-21 19:22:13.785][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-21 19:22:13.787][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-21 19:22:13.788][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-21 19:22:13.790][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-21 19:22:13.792][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-21 19:22:13.794][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-21 19:22:13.795][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-21 19:22:13.797][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-21 19:22:13.799][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-21 19:22:13.800][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-21 19:22:13.802][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-21 19:22:13.803][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-21 19:22:13.805][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-21 19:22:13.806][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-21 19:22:13.808][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-21 19:22:13.810][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-21 19:22:13.812][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-21 19:22:13.814][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-21 19:22:13.816][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-21 19:22:13.818][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-21 19:22:13.825][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-21 19:22:13.828][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-21 19:22:13.832][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 19:22:13.833][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.838][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:13.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:13.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:13.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:13.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:13.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:13.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.879][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[2025-04-21 19:22:13.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:13.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:13.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:13.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:13.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.895][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[2025-04-21 19:22:13.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:13.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:13.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:13.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:13.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:13.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:13.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:13.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:13.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:13.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:13.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:13.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:13.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:13.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:13.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:13.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:13.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.970][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[2025-04-21 19:22:13.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:13.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:13.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:13.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:13.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:13.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:13.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:13.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:13.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:13.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:13.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:22:13.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:13.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:13.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:14.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:14.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:14.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:14.009][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-21 19:22:14.023][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-21 19:22:14.028][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 19:22:14.030][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-21 19:22:14.031][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 19:22:14.033][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 19:22:14.034][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 19:22:14.035][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 19:22:14.036][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-21 19:22:14.037][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-21 19:22:14.039][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-21 19:22:14.040][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 19:22:14.041][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 19:22:14.042][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-21 19:22:14.043][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 19:22:14.045][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-21 19:22:14.045][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-21 19:22:14.045][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-21 19:22:14.045][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-21 19:22:14.045][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-21 19:22:14.045][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-21 19:22:14.045][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-21 19:22:14.045][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-21 19:22:14.045][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-21 19:22:14.045][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-21 19:22:14.045][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-21 19:22:14.047][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-21 19:22:14.048][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 19:22:14.048][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 19:22:14.048][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 19:22:14.049][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-21 19:22:14.051][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:22:14.052][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:22:14.053][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 19:22:14.054][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:22:14.055][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:22:14.057][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 19:22:14.058][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:14.058][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-21 19:22:14.059][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 19:22:14.060][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 19:22:14.062][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-21 19:22:14.063][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-21 19:22:14.063][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-21 19:22:14.072][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-21 19:22:14.074][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-21 19:22:14.076][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-21 19:22:14.078][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-21 19:22:14.079][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-21 19:22:14.081][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-21 19:22:14.115][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-21 19:22:14.117][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-21 19:22:14.123][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-21 19:22:14.130][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-21 19:22:14.174][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-21 19:22:14.176][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-21 19:22:14.178][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-21 19:22:14.180][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-21 19:22:14.192][biodb::testThat]
biodb.INFO [2025-04-21 19:22:14.193][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-04-21 19:22:14.195][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:22:14.196][biodb::testThat]
biodb.TRACE[2025-04-21 19:22:14.201][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[2025-04-21 19:22:14.207][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:14.211][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:14.221][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:14.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:14.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:14.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:14.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:14.246][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:14.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:14.258][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:14.260][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:14.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.263][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:14.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:14.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.288][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:14.290][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:14.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.292][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.326][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:14.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:14.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.332][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:14.334][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:14.335][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.336][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.338][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:14.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:14.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.344][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:14.345][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:14.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.347][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.349][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:14.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:14.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.354][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:14.356][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:14.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.358][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.360][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:14.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:14.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.366][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:14.367][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:14.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.370][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.372][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:14.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:14.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.377][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:14.378][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:14.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.380][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.382][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:14.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:14.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.388][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:14.390][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:14.391][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.392][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:14.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:14.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.400][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:14.401][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:14.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.404][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.416][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:14.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:14.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.422][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:14.424][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:14.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.429][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.434][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:14.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:14.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.440][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:14.442][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:14.443][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.445][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.447][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:14.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:14.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:14.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:14.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:14.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:14.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:14.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:14.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:14.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:14.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:14.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:14.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:14.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:14.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:14.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:14.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:14.562][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-04-21 19:22:14.566][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:14.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:14.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:14.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:14.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.614][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:14.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:14.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.629][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:14.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:14.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:14.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:14.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:14.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:14.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.650][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-21 19:22:14.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-21 19:22:14.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.655][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-21 19:22:14.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-21 19:22:14.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.662][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-21 19:22:14.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-21 19:22:14.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.670][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-21 19:22:14.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-21 19:22:14.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:14.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:14.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.727][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:14.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:14.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:14.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:14.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:14.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:14.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:14.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:14.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:14.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:14.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:14.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:14.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:14.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:14.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:14.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:14.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:14.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:14.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.840][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:14.842][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:14.843][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.844][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:14.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:14.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.889][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.896][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.898][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.899][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.901][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:14.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.927][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:14.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:14.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.934][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:14.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:14.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.941][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:14.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:14.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.946][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:14.948][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:14.949][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.951][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.952][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:14.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:14.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.971][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:14.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:14.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.978][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:14.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:14.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.984][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:14.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:14.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.992][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:14.994][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:14.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:14.997][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:14.998][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:14.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:15.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:15.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:15.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:15.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:15.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.027][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:15.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:15.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.036][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:15.038][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:15.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.040][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.042][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:15.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:15.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.059][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:15.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:15.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:15.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:15.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:15.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:15.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.079][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:15.080][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:15.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.083][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:15.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:15.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.101][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:15.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:15.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.107][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:15.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:15.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.113][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:15.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:15.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.122][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:15.124][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:15.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.134][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.136][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:15.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:15.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.153][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-21 19:22:15.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:15.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.159][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-21 19:22:15.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:15.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.169][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-21 19:22:15.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:15.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.175][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-21 19:22:15.177][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:15.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.179][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.181][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-21 19:22:15.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:15.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.206][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:15.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:15.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.213][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:15.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:15.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.219][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:15.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:15.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.227][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:15.229][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:15.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.235][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.238][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:15.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:15.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.255][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:15.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:15.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.262][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:15.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:15.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.268][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:15.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:15.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.273][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:15.274][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:15.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.277][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.279][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:15.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:15.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.297][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:15.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:15.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.305][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:15.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:15.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.312][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:15.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:15.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.321][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:15.324][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:15.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.327][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.329][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:15.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:15.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.348][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:15.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:15.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.355][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:15.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:15.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.361][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:15.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:15.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.367][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:15.368][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:15.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.375][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.376][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:15.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:15.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.402][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:15.404][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:15.406][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.407][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.416][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:15.418][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:15.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.421][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.429][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:15.431][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:15.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.433][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.441][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:15.446][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:15.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.449][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.456][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:15.458][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:15.459][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.461][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.472][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:15.474][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:15.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.477][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.486][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:15.488][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:15.489][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.491][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.499][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:15.501][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:15.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.504][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.518][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-21 19:22:15.520][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:15.521][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.523][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.531][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:15.535][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:15.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.538][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.547][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:15.549][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:15.551][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.552][ef$get] fields variable is a list.
biodb.INFO [2025-04-21 19:22:15.566][biodb::testThat]
biodb.INFO [2025-04-21 19:22:15.568][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-04-21 19:22:15.569][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:22:15.571][biodb::testThat]
biodb.DEBUG[2025-04-21 19:22:15.591][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-04-21 19:22:15.600][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:15.608][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-04-21 19:22:15.610][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 19:22:15.613][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-04-21 19:22:15.615][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:15.658][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:15.660][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:15.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:15.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:15.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:15.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:15.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:15.682][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:15.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:15.686][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:15.688][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:15.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.691][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:15.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:15.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.723][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:15.725][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:15.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.728][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.730][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:15.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:15.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.735][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:15.738][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:15.741][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.745][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.747][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:15.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:15.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.753][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:15.754][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:15.756][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.758][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.759][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:15.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:15.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.766][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:15.767][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:15.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.770][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.772][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:15.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:15.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.778][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:15.779][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:15.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.782][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.784][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:15.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:15.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.792][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:15.794][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:15.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.797][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.799][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:15.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:15.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.805][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:15.806][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:15.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.811][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:15.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:15.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.822][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:15.824][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:15.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.827][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.829][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:15.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:15.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.836][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:15.837][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:15.838][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.840][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.842][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:15.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:15.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.848][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:15.849][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:15.850][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.852][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.854][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:15.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:15.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:15.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:15.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:15.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:15.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:15.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:15.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:15.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:15.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:15.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:15.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:15.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:15.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:15.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:15.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:15.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:15.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:15.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:15.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:15.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:15.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:15.938][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-04-21 19:22:15.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-21 19:22:15.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-21 19:22:15.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-21 19:22:15.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-21 19:22:15.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:15.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-21 19:22:15.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-21 19:22:15.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-21 19:22:15.973][biodb::testThat]
biodb.INFO [2025-04-21 19:22:15.974][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-04-21 19:22:15.976][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:22:15.977][biodb::testThat]
biodb.TRACE[2025-04-21 19:22:15.982][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:15.985][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:15.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:15.988][ef$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:15.990][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-04-21 19:22:16.035][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:16.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:16.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:16.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:16.042][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:16.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:16.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:16.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:16.048][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:16.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:16.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:16.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:16.058][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-04-21 19:22:16.065][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-21 19:22:16.095][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 19:22:16.129][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-04-21 19:22:16.131][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 19:22:16.134][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-04-21 19:22:16.168][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[2025-04-21 19:22:16.172][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:16.174][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:16.177][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-21 19:22:16.746][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-21 19:22:17.180][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:17.184][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-04-21 19:22:17.203][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-04-21 19:22:17.207][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-04-21 19:22:17.227][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:17.229][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:17.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.232][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.233][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:17.235][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:17.236][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.237][ef$get] fields variable is a list.
biodb.INFO [2025-04-21 19:22:17.250][biodb::testThat]
biodb.INFO [2025-04-21 19:22:17.252][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-04-21 19:22:17.254][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:22:17.255][biodb::testThat]
biodb.TRACE[2025-04-21 19:22:17.290][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:17.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:17.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.297][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:17.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:17.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.319][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:17.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:17.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:17.407][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 19:22:17.412][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 19:22:17.416][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-21 19:22:17.418][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 19:22:17.420][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-04-21 19:22:17.447][biodb::testThat]
biodb.INFO [2025-04-21 19:22:17.449][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-04-21 19:22:17.450][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:22:17.451][biodb::testThat]
biodb.TRACE[2025-04-21 19:22:17.493][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:17.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:17.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.500][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:17.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:17.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.506][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:17.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:17.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.511][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:17.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:17.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:17.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:17.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.524][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:17.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:17.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.536][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-21 19:22:17.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-21 19:22:17.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.543][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-21 19:22:17.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-21 19:22:17.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.548][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-21 19:22:17.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-21 19:22:17.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.557][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-21 19:22:17.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-21 19:22:17.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.587][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:17.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:17.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:17.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:17.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.603][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:17.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:17.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.609][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:17.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:17.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:17.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:17.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.625][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:17.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:17.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.631][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-21 19:22:17.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-21 19:22:17.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.637][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-21 19:22:17.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-21 19:22:17.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.643][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-21 19:22:17.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-21 19:22:17.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:17.655][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-21 19:22:17.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-21 19:22:17.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:17.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-21 19:22:17.670][biodb::testThat]
biodb.INFO [2025-04-21 19:22:17.672][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-04-21 19:22:17.678][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:22:17.680][biodb::testThat]
biodb.INFO [2025-04-21 19:22:17.693][biodb::testThat]
biodb.INFO [2025-04-21 19:22:17.697][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-04-21 19:22:17.701][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:22:17.702][biodb::testThat]
biodb.INFO [2025-04-21 19:22:17.716][biodb::testThat]
biodb.INFO [2025-04-21 19:22:17.718][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-04-21 19:22:17.719][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:22:17.720][biodb::testThat]
biodb.DEBUG[2025-04-21 19:22:17.726][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-04-21 19:22:18.391][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-04-21 19:22:19.404][biodb::testThat]
biodb.INFO [2025-04-21 19:22:19.406][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-04-21 19:22:19.407][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:22:19.408][biodb::testThat]
biodb.DEBUG[2025-04-21 19:22:19.759][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[2025-04-21 19:22:20.112][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:20.114][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:20.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:20.117][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:20.118][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:20.120][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:20.121][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:20.123][ef$get] fields variable is a list.
biodb.INFO [2025-04-21 19:22:20.125][biodb::testThat]
biodb.INFO [2025-04-21 19:22:20.126][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2025-04-21 19:22:20.127][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:22:20.128][biodb::testThat]
biodb.TRACE[2025-04-21 19:22:20.146][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:20.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:20.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:20.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:20.153][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:20.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:20.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:20.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:20.158][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:20.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:20.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:20.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:20.278][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 19:22:20.283][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 19:22:20.286][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-21 19:22:20.287][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 19:22:20.289][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-21 19:22:20.380][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 19:22:20.384][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 19:22:20.387][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-21 19:22:20.388][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 19:22:20.390][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-04-21 19:22:20.413][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-21 19:22:20.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-21 19:22:20.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:20.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:20.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:20.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:20.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:20.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:20.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:20.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:20.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:20.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:20.442][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:20.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:20.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:20.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:20.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:20.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:20.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:20.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:20.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:20.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:20.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:20.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:20.471][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 19:22:20.500][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:20.502][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:20.522][private$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[2025-04-21 19:22:20.863][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[2025-04-21 19:22:21.196][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:21.200][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-04-21 19:22:21.206][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-04-21 19:22:21.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:21.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:21.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:21.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:21.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:21.222][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:21.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:21.225][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-04-21 19:22:21.302][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:21.305][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-04-21 19:22:21.307][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:21.308][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:21.309][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:21.316][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:21.317][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:21.318][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:21.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:21.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:21.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:21.333][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:21.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:21.336][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:21.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:21.339][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-04-21 19:22:21.343][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:21.346][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:21.349][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-04-21 19:22:21.684][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-04-21 19:22:22.025][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:22.028][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-04-21 19:22:22.033][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-04-21 19:22:22.037][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-04-21 19:22:22.039][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:22.042][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:22.043][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:22.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:22.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:22.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:22.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:22.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:22.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:22.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:22.063][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:22.065][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:22.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.067][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:22.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:22.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.073][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:22.074][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:22.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.076][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.078][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:22.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:22.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.083][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:22.084][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:22.085][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.092][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.099][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:22.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:22.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.104][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:22.106][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:22.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.108][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.110][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:22.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:22.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.114][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:22.120][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:22.122][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.123][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.124][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:22.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:22.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.129][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:22.131][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:22.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.133][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.134][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:22.136][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:22.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.139][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.143][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:22.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:22.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.149][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:22.150][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:22.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.152][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:22.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:22.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.159][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:22.160][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:22.161][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.162][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.164][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:22.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:22.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.169][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:22.170][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:22.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.173][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.174][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:22.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:22.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.179][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:22.181][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:22.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.183][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.185][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:22.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:22.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:22.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:22.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:22.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:22.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:22.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:22.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:22.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:22.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:22.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:22.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:22.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:22.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:22.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:22.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:22.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:22.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:22.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:22.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:22.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:22.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:22.244][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-04-21 19:22:22.253][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:22.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:22.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:22.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:22.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:22.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:22.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:22.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:22.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:22.274][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[2025-04-21 19:22:22.279][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:22.281][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:22.283][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-21 19:22:22.619][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-21 19:22:23.044][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:23.047][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-04-21 19:22:23.052][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-04-21 19:22:23.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:23.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:23.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:23.081][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:23.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:23.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:23.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:23.085][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:23.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:23.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:23.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:23.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:23.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:23.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:23.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:23.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:23.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:23.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:23.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:23.099][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:23.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:23.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:23.119][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:23.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:23.128][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:23.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:23.131][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-04-21 19:22:23.133][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:23.135][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-04-21 19:22:23.137][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:23.138][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:23.140][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:23.141][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:23.143][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:23.145][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:23.164][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:23.166][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:23.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:23.175][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:23.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:23.177][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:23.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:23.179][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-04-21 19:22:23.182][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:23.183][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:23.185][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-04-21 19:22:23.516][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-04-21 19:22:23.854][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:23.858][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-04-21 19:22:23.864][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-04-21 19:22:23.869][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-04-21 19:22:23.872][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:23.873][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:23.874][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:23.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:23.876][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:23.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:23.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:23.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:23.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:23.888][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[2025-04-21 19:22:23.891][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:23.893][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:23.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:23.895][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:23.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:23.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:23.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:23.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:23.902][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:23.903][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:23.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:23.905][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:23.906][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:23.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:23.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:23.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:23.911][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:23.922][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:23.924][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:23.925][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:23.927][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:23.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:23.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:23.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:23.933][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:23.934][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:23.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:23.937][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:23.938][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:23.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:23.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:23.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:23.944][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:23.945][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:23.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:23.947][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:23.949][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:23.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:23.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:23.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:23.954][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:23.955][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:23.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:23.958][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:23.960][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:23.961][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:23.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:23.963][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:23.964][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:23.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:23.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:23.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:23.969][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:23.971][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:23.972][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:23.973][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:23.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:23.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:23.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:23.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:23.979][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:23.981][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:23.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:23.983][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:23.985][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:23.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:23.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:23.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:23.991][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:23.992][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:23.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:23.995][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:23.997][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:23.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:23.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.001][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:24.003][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:24.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.006][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.008][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:24.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:24.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:24.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:24.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:24.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:24.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:24.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:24.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:24.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:24.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:24.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:24.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:24.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:24.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:24.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:24.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:24.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:24.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:24.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:24.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:24.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:24.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:24.098][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-04-21 19:22:24.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:24.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:24.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.105][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:24.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:24.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:24.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:24.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:24.143][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 19:22:24.147][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 19:22:24.149][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-21 19:22:24.151][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 19:22:24.153][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-21 19:22:24.156][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:24.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:24.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:24.166][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:24.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:24.169][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:24.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:24.171][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:24.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:24.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.176][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:24.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:24.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:24.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:24.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:24.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:24.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:24.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:24.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:24.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:24.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:24.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:24.201][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-04-21 19:22:24.203][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:24.205][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-04-21 19:22:24.206][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:24.208][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:24.209][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:24.210][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:24.211][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:24.213][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:24.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:24.223][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:24.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:24.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:24.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:24.234][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:24.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:24.237][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-04-21 19:22:24.241][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:24.242][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:24.244][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-04-21 19:22:24.578][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-04-21 19:22:24.914][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:24.918][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-04-21 19:22:24.922][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-04-21 19:22:24.925][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-04-21 19:22:24.928][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:24.930][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:24.931][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:24.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:24.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:24.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:24.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:24.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:24.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:24.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:24.949][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:24.950][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:24.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.952][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:24.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:24.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.959][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:24.960][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:24.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.962][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.964][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:24.965][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:24.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.967][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.969][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:24.970][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:24.971][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.972][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.973][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:24.974][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:24.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.976][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.978][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:24.980][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:24.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.981][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.983][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:24.984][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:24.985][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.986][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.988][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:24.989][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:24.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.991][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.992][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:24.993][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:24.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:24.996][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:24.998][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:24.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:25.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:25.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:25.002][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:25.003][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:25.004][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:25.005][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:25.007][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:25.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:25.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:25.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:25.011][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:25.012][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:25.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:25.026][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:25.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:25.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:25.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:25.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:25.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:25.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:25.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:25.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:25.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:25.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:25.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:25.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:25.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:25.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:25.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:25.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:25.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:25.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:25.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:25.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:25.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:25.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:25.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:25.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:25.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:25.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:25.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:25.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:25.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:25.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:25.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:25.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:25.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:25.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:25.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:25.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:25.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:25.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:25.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:25.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:25.077][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-04-21 19:22:25.078][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:25.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:25.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:25.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:25.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:25.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:25.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:25.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:25.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:25.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:25.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:25.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:25.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:25.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:25.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:25.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:25.109][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:25.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:25.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:25.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:25.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:25.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:25.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:25.125][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:25.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:25.127][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:25.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:25.129][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-04-21 19:22:25.131][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:25.133][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-04-21 19:22:25.134][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:25.136][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:25.137][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:25.138][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:25.139][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:25.140][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:25.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:25.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:25.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:25.153][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:25.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:25.156][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:25.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:25.159][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-04-21 19:22:25.170][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:25.171][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:25.174][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-04-21 19:22:25.508][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-04-21 19:22:25.974][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:25.977][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-04-21 19:22:25.983][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-04-21 19:22:25.987][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-04-21 19:22:25.989][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:25.991][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:25.993][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:25.996][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:25.997][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:25.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:26.006][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:26.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:26.009][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:26.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:26.012][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:26.014][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:26.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.016][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:26.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:26.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.022][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:26.023][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:26.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.026][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.027][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:26.029][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:26.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.032][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.034][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:26.035][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:26.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.038][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.039][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:26.041][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:26.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.043][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.044][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:26.046][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:26.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.048][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.050][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:26.051][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:26.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.054][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.056][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:26.057][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:26.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.060][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.062][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:26.063][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:26.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.066][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.068][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:26.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:26.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.074][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:26.075][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:26.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.077][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.079][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:26.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:26.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.084][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:26.086][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:26.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.088][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:26.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:26.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:26.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:26.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:26.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:26.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:26.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:26.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:26.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:26.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:26.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:26.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:26.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:26.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:26.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:26.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:26.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:26.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:26.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:26.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:26.157][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-04-21 19:22:26.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:26.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:26.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.164][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:26.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:26.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:26.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:26.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:26.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:26.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:26.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:26.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:26.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:26.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:26.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:26.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:26.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:26.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:26.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:26.202][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-04-21 19:22:26.204][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:26.206][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-04-21 19:22:26.208][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:26.209][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:26.211][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:26.212][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:26.214][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:26.215][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:26.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:26.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:26.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:26.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:26.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:26.233][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:26.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:26.236][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-04-21 19:22:26.239][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:26.241][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:26.242][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-04-21 19:22:26.576][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-04-21 19:22:26.912][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:26.916][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-04-21 19:22:26.932][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-04-21 19:22:26.936][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-04-21 19:22:26.938][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:26.940][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:26.942][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:26.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:26.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:26.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:26.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:26.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:26.956][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:26.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:26.960][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:26.962][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:26.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.964][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:26.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:26.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.971][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:26.973][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:26.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.975][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.977][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:26.978][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:26.980][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.981][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.983][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:26.984][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:26.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.987][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.988][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:26.990][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:26.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.992][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.993][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:26.995][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:26.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:26.998][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:26.999][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:27.000][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:27.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.002][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:27.004][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:27.005][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:27.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.008][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:27.009][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:27.010][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:27.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.013][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:27.015][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:27.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:27.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:27.020][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:27.021][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:27.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.024][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:27.025][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:27.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:27.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:27.031][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:27.032][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:27.033][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.034][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:27.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:27.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:27.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:27.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:27.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:27.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:27.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:27.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:27.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:27.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:27.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:27.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:27.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:27.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:27.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:27.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:27.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:27.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:27.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:27.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:27.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:27.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:27.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:27.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:27.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:27.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:27.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:27.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:27.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:27.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:27.094][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-04-21 19:22:27.096][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:27.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:27.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:27.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:27.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:27.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:27.105][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:27.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:27.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:27.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:27.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:27.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:27.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:27.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:27.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:27.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:27.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:27.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:27.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:27.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:27.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:27.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:27.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:27.132][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-04-21 19:22:27.134][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:27.136][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-04-21 19:22:27.137][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:27.139][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:27.140][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:27.141][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:27.142][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:27.144][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:27.147][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:27.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:27.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:27.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:27.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:27.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:27.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:27.163][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-04-21 19:22:27.167][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:27.168][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:27.170][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-04-21 19:22:27.507][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-04-21 19:22:28.098][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:28.102][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-04-21 19:22:28.107][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-04-21 19:22:28.111][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-04-21 19:22:28.114][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:28.116][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:28.118][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:28.132][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:28.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:28.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:28.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:28.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:28.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:28.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:28.149][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:28.151][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:28.152][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.153][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:28.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:28.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.159][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:28.160][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:28.161][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.162][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.164][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:28.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:28.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.168][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:28.169][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:28.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.172][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.174][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:28.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:28.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.180][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:28.181][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:28.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.183][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.185][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:28.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:28.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.190][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:28.192][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:28.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.194][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.196][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:28.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:28.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.201][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:28.202][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:28.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.204][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.205][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:28.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:28.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.210][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:28.211][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:28.213][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.214][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.215][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:28.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:28.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.221][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:28.222][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:28.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.224][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:28.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:28.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.231][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:28.232][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:28.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.235][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.238][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:28.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:28.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.243][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:28.244][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:28.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.247][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.248][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:28.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:28.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.254][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:28.256][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:28.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.266][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.268][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:28.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:28.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:28.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:28.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:28.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:28.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:28.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:28.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:28.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:28.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:28.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:28.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:28.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:28.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:28.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:28.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:28.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:28.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:28.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:28.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:28.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:28.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:28.324][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-04-21 19:22:28.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:28.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:28.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:28.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:28.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:28.336][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:28.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:28.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:28.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:28.341][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:28.342][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:28.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:28.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:28.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:28.354][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:28.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:28.357][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-04-21 19:22:28.359][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:28.361][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-04-21 19:22:28.363][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:28.364][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:28.365][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:28.367][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:28.368][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:28.369][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:28.373][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:28.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:28.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:28.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:28.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:28.386][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:28.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:28.389][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-04-21 19:22:28.392][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:28.394][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:28.404][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-04-21 19:22:28.738][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-04-21 19:22:29.082][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:29.085][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-04-21 19:22:29.091][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-04-21 19:22:29.095][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-04-21 19:22:29.097][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:29.099][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:29.101][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:29.104][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:29.105][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:29.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:29.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:29.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:29.117][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:29.118][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.TRACE[2025-04-21 19:22:29.122][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:29.123][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:29.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.126][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:29.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:29.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.133][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:29.135][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:29.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.137][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.139][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:29.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:29.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.144][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:29.145][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:29.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.147][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.149][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:29.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:29.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.154][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:29.156][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:29.157][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.158][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.160][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:29.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:29.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.165][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:29.167][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:29.168][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.169][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.171][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:29.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:29.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.176][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:29.178][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:29.179][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.180][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.182][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:29.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:29.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.203][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:29.205][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:29.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.207][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.209][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:29.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:29.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.214][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:29.215][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:29.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.218][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:29.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:29.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.224][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:29.225][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:29.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.235][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.242][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:29.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:29.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.248][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:29.250][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:29.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.252][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.254][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:29.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:29.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.259][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:29.260][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:29.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.262][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.264][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:29.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:29.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.269][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:29.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:29.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:29.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:29.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:29.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:29.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:29.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:29.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:29.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:29.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:29.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:29.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:29.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:29.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:29.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:29.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:29.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:29.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:29.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:29.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:29.320][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-04-21 19:22:29.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:29.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:29.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:29.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:29.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:29.332][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:29.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:29.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:29.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:29.338][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:29.339][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:29.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:29.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:29.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:29.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:29.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:29.352][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-04-21 19:22:29.353][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:29.356][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-04-21 19:22:29.357][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:29.359][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:29.360][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:29.362][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:29.363][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:29.364][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:29.375][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:29.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:29.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:29.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:29.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:29.388][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:29.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:29.391][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-04-21 19:22:29.394][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:29.395][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:29.397][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-04-21 19:22:29.735][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-04-21 19:22:30.094][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:30.097][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-04-21 19:22:30.102][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-04-21 19:22:30.105][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-04-21 19:22:30.107][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:30.109][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:30.110][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:30.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:30.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:30.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:30.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:30.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:30.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:30.123][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.TRACE[2025-04-21 19:22:30.125][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:30.127][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:30.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.128][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:30.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:30.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.134][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:30.135][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:30.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.138][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.140][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:30.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:30.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.145][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:30.147][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:30.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.149][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.150][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:30.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:30.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.155][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:30.157][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:30.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.159][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.161][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:30.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:30.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.165][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:30.166][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:30.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.169][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.170][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:30.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:30.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.175][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:30.176][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:30.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.178][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.179][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:30.181][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:30.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.183][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.184][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:30.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:30.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.201][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:30.203][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:30.205][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.206][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:30.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:30.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.213][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:30.214][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:30.215][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.216][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.218][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:30.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:30.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.223][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:30.224][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:30.225][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.226][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.228][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:30.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:30.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.232][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:30.234][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:30.235][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.236][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.238][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:30.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:30.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:30.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:30.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:30.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:30.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:30.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:30.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:30.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:30.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:30.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:30.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:30.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:30.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:30.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:30.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:30.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:30.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:30.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:30.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:30.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:30.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:30.291][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-04-21 19:22:30.293][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:30.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:30.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:30.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:30.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:30.322][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:30.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:30.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:30.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:30.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:30.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:30.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:30.338][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:30.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:30.347][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:30.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:30.351][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-04-21 19:22:30.352][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:30.355][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-04-21 19:22:30.356][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:30.358][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:30.359][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:30.360][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:30.362][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:30.363][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:30.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:30.367][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:30.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:30.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:30.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:30.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:30.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:30.382][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-04-21 19:22:30.386][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:30.387][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:30.389][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-04-21 19:22:30.724][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-04-21 19:22:31.101][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:31.104][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-04-21 19:22:31.109][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-04-21 19:22:31.113][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-04-21 19:22:31.115][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:31.116][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:31.118][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:31.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:31.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:31.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:31.127][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:31.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:31.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:31.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:31.134][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:31.135][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:31.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.138][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:31.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:31.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.146][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:31.163][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:31.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.167][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.169][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:31.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:31.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.183][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:31.184][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:31.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.187][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.189][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:31.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:31.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.196][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:31.197][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:31.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.199][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.201][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:31.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:31.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.206][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:31.207][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:31.209][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.210][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.211][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:31.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:31.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.227][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:31.228][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:31.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.231][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.232][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:31.233][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:31.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.235][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.237][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:31.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:31.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.242][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:31.243][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:31.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.245][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:31.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:31.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.252][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:31.253][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:31.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.255][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.256][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:31.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:31.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.261][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:31.262][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:31.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.264][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.265][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:31.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:31.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.270][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:31.271][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:31.272][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.273][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.274][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:31.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:31.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:31.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:31.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:31.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:31.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:31.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:31.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:31.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:31.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:31.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:31.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:31.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:31.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:31.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:31.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:31.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:31.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:31.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:31.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:31.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:31.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:31.329][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-04-21 19:22:31.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:31.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:31.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:31.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:31.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:31.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:31.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:31.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:31.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:31.353][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:31.354][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:31.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:31.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:31.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:31.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:31.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:31.367][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-04-21 19:22:31.369][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:31.370][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-04-21 19:22:31.372][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:31.373][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:31.375][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:31.376][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:31.377][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:31.378][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:31.382][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:31.383][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:31.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:31.393][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:31.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:31.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:31.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:31.399][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-04-21 19:22:31.403][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:31.404][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:31.406][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-04-21 19:22:31.740][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-04-21 19:22:32.078][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:32.080][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-04-21 19:22:32.085][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-04-21 19:22:32.088][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-04-21 19:22:32.090][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:32.091][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:32.092][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:32.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:32.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:32.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:32.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:32.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:32.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:32.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:32.110][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:32.111][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:32.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.114][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:32.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:32.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.121][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:32.122][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:32.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.125][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.126][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:32.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:32.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.130][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:32.132][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:32.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.134][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.136][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:32.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:32.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.140][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:32.142][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:32.154][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.155][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.158][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:32.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:32.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.164][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:32.165][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:32.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.167][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.169][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:32.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:32.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.175][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:32.176][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:32.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.178][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.180][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:32.181][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:32.183][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.184][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.186][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:32.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:32.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.190][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:32.192][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:32.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.194][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.196][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:32.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:32.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.201][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:32.202][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:32.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.204][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.206][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:32.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:32.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.210][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:32.211][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:32.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.213][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.214][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:32.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:32.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.218][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:32.220][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:32.221][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.222][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.223][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:32.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:32.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:32.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:32.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:32.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:32.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:32.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:32.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:32.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:32.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:32.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:32.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:32.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:32.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:32.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:32.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:32.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:32.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:32.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:32.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:32.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:32.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:32.287][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-04-21 19:22:32.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:32.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:32.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:32.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:32.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:32.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:32.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:32.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:32.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:32.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:32.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:32.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:32.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:32.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:32.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:32.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:32.320][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-04-21 19:22:32.322][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:32.324][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-04-21 19:22:32.326][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:32.328][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:32.329][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:32.331][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:32.332][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:32.333][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:32.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:32.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:32.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:32.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:32.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:32.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:32.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:32.350][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-04-21 19:22:32.353][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:32.354][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:32.356][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-04-21 19:22:32.789][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-04-21 19:22:33.125][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:33.128][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-04-21 19:22:33.134][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-04-21 19:22:33.137][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-04-21 19:22:33.139][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:33.140][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:33.141][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:33.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:33.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:33.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:33.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:33.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:33.154][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:33.155][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.TRACE[2025-04-21 19:22:33.158][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:33.159][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:33.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.161][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:33.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:33.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.168][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:33.169][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:33.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.171][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.182][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:33.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:33.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.189][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:33.190][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:33.191][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.192][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.194][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:33.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:33.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.199][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:33.200][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:33.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.202][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.204][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:33.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:33.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.209][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:33.210][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:33.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.212][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.213][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:33.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:33.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.218][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:33.219][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:33.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.221][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.222][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:33.223][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:33.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.225][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.226][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:33.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:33.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.232][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:33.233][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:33.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.236][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:33.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:33.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.243][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:33.244][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:33.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.247][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.248][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:33.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:33.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.254][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:33.255][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:33.256][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.257][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.259][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:33.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:33.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.264][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:33.265][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:33.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.267][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.268][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:33.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:33.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:33.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:33.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:33.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:33.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:33.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:33.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:33.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:33.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:33.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:33.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:33.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:33.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:33.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:33.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:33.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:33.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:33.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:33.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:33.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:33.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:33.326][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-04-21 19:22:33.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:33.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:33.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:33.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:33.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:33.336][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:33.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:33.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:33.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:33.340][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:33.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:33.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:33.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:33.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:33.351][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:33.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:33.353][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-04-21 19:22:33.354][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:33.356][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-04-21 19:22:33.358][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:33.359][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:33.361][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:33.363][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:33.365][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:33.367][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:33.372][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:33.373][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:33.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:33.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:33.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:33.384][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:33.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:33.386][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-04-21 19:22:33.390][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:33.391][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:33.393][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-04-21 19:22:33.731][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-04-21 19:22:34.091][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:34.094][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-04-21 19:22:34.099][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-04-21 19:22:34.103][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-04-21 19:22:34.105][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:34.106][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:34.107][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:34.109][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:34.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:34.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:34.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:34.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:34.125][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:34.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:34.141][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:34.143][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:34.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.146][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:34.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:34.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.153][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:34.155][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:34.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.157][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.159][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:34.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:34.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.165][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:34.166][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:34.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.169][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.170][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:34.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:34.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.175][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:34.176][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:34.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.178][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.179][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:34.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:34.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.184][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:34.185][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:34.186][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.187][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.189][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:34.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:34.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.193][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:34.194][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:34.195][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.196][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.198][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:34.199][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:34.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.202][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.203][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:34.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:34.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.208][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:34.209][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:34.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.211][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:34.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:34.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.217][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:34.218][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:34.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.220][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.221][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:34.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:34.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.226][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:34.227][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:34.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.229][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.230][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:34.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:34.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.235][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:34.236][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:34.237][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.238][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.239][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:34.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:34.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:34.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:34.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:34.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:34.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:34.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:34.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:34.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:34.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:34.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:34.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:34.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:34.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:34.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:34.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:34.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:34.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:34.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:34.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:34.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:34.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:34.307][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-04-21 19:22:34.308][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:34.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:34.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.313][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:34.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:34.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:34.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:34.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:34.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:34.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:34.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:34.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:34.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:34.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:34.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:34.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:34.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:34.335][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-04-21 19:22:34.336][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:34.338][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-04-21 19:22:34.339][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:34.341][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:34.342][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:34.343][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:34.344][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:34.345][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:34.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:34.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:34.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:34.356][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:34.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:34.359][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:34.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:34.362][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-04-21 19:22:34.365][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:34.366][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:34.367][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-04-21 19:22:34.702][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-04-21 19:22:35.040][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:35.042][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-04-21 19:22:35.047][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-04-21 19:22:35.057][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-04-21 19:22:35.062][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:35.064][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:35.065][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:35.067][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:35.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:35.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:35.076][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:35.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:35.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:35.080][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.TRACE[2025-04-21 19:22:35.082][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:35.083][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:35.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.085][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:35.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:35.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.090][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:35.091][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:35.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.093][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.094][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:35.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:35.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.099][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:35.100][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:35.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.103][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.105][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:35.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:35.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.110][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:35.111][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:35.111][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.112][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.114][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:35.115][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:35.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.116][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.118][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:35.119][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:35.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.121][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.122][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:35.123][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:35.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.125][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.126][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:35.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:35.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.130][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:35.131][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:35.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.133][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.134][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:35.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:35.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.138][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:35.139][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:35.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.140][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.142][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:35.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:35.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.147][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:35.148][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:35.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.150][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.151][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:35.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:35.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.156][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:35.157][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:35.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.159][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:35.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:35.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.165][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:35.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:35.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:35.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:35.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:35.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:35.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:35.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:35.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:35.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:35.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:35.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:35.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:35.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:35.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:35.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:35.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:35.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:35.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:35.215][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-04-21 19:22:35.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:35.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:35.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.220][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:35.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:35.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:35.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:35.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:35.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:35.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:35.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:35.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:35.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:35.238][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:35.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:35.240][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-04-21 19:22:35.241][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:35.243][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-04-21 19:22:35.244][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:35.246][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:35.247][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:35.248][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:35.249][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:35.251][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:35.253][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:35.254][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:35.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:35.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:35.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:35.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:35.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:35.266][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-04-21 19:22:35.268][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:35.269][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:35.270][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-04-21 19:22:35.607][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-04-21 19:22:35.944][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:35.946][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-04-21 19:22:35.950][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-04-21 19:22:35.954][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-04-21 19:22:35.965][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:35.967][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:35.969][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:35.971][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:35.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:35.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:35.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:35.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:35.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:35.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:35.986][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:35.987][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:35.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.989][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:35.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:35.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:35.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:35.996][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:35.998][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:35.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.000][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.001][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:36.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:36.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.006][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:36.007][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:36.008][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.009][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.011][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:36.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:36.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.031][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:36.033][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:36.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.035][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.037][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:36.038][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:36.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.041][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.043][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:36.045][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:36.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.049][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.054][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:36.058][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:36.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.061][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.063][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:36.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:36.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.069][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:36.070][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:36.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.073][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:36.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:36.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.081][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:36.083][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:36.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.085][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.086][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:36.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:36.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.091][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:36.093][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:36.094][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.095][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.097][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:36.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:36.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.102][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:36.103][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:36.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.106][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:36.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:36.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.114][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:36.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:36.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:36.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:36.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:36.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:36.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:36.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:36.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:36.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:36.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:36.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:36.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:36.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:36.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:36.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:36.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:36.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:36.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:36.163][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-04-21 19:22:36.164][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:36.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:36.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:36.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:36.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.174][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:36.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:36.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:36.180][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:36.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:36.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:36.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:36.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:36.192][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:36.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:36.194][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-04-21 19:22:36.196][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:36.198][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-04-21 19:22:36.200][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:36.201][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:36.203][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:36.204][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:36.205][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:36.206][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:36.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:36.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:36.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:36.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:36.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:36.222][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:36.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:36.224][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-04-21 19:22:36.227][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:36.228][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:36.230][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-04-21 19:22:36.575][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-04-21 19:22:36.915][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:36.918][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-04-21 19:22:36.924][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-04-21 19:22:36.941][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-04-21 19:22:36.944][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:36.946][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:36.948][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:36.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:36.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:36.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:36.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:36.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:36.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:36.965][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[2025-04-21 19:22:36.969][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:36.970][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:36.972][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.973][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:36.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:36.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.980][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:36.982][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:36.983][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.985][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.986][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:36.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:36.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.992][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:36.994][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:36.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:36.997][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:36.999][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:37.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:37.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.005][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:37.006][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:37.008][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.009][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.011][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:37.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:37.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.017][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:37.018][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:37.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.021][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.022][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:37.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:37.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.028][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:37.029][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:37.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.032][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.034][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:37.036][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:37.037][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.038][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.040][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:37.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:37.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.046][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:37.047][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:37.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.049][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:37.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:37.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.057][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:37.059][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:37.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.061][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.063][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:37.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:37.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.069][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:37.070][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:37.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.073][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.075][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:37.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:37.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.081][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:37.090][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:37.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.094][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.096][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:37.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:37.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:37.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:37.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.107][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:37.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:37.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:37.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:37.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:37.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:37.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:37.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:37.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:37.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:37.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:37.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:37.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:37.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:37.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:37.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:37.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:37.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:37.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:37.162][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-04-21 19:22:37.164][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:37.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:37.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:37.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:37.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:37.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:37.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:37.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:37.186][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:37.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:37.194][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:37.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:37.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:37.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:37.200][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-04-21 19:22:37.201][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:37.203][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-04-21 19:22:37.205][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:37.207][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:37.208][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:37.209][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:37.211][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:37.212][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:37.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:37.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:37.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:37.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:37.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:37.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:37.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:37.231][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-04-21 19:22:37.241][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:37.243][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:37.246][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-04-21 19:22:37.580][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-04-21 19:22:37.924][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:37.930][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-04-21 19:22:37.935][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-04-21 19:22:37.940][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-04-21 19:22:37.942][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:37.944][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:37.945][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:37.948][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:37.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:37.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:37.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:37.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:37.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:37.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:37.965][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:37.967][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:37.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.970][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:37.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:37.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.977][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:37.979][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:37.980][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.981][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.983][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:37.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:37.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.989][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:37.990][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:37.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.993][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:37.995][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:37.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:37.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:37.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.000][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:38.002][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:38.003][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.004][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.006][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:38.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:38.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.012][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:38.013][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:38.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.016][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.018][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:38.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:38.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.023][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:38.024][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:38.026][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.027][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.029][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:38.030][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:38.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.033][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.035][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:38.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:38.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.040][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:38.041][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:38.043][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.044][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:38.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:38.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.052][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:38.054][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:38.055][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.064][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.071][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:38.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:38.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.078][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:38.080][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:38.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.082][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.084][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:38.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:38.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.090][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:38.091][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:38.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.094][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.096][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:38.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:38.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.101][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:38.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:38.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.107][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:38.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:38.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:38.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:38.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:38.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:38.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:38.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:38.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:38.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:38.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:38.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:38.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:38.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:38.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:38.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:38.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:38.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:38.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:38.156][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-04-21 19:22:38.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:38.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:38.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:38.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:38.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.169][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:38.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:38.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:38.174][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:38.175][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:38.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:38.184][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:38.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:38.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:38.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:38.190][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-04-21 19:22:38.192][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:38.194][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-04-21 19:22:38.196][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:38.197][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:38.199][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:38.200][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:38.202][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:38.203][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:38.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:38.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:38.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:38.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:38.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:38.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:38.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:38.231][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-04-21 19:22:38.235][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:38.236][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:38.239][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-04-21 19:22:38.575][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-04-21 19:22:38.930][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:38.933][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-04-21 19:22:38.938][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-04-21 19:22:38.942][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-04-21 19:22:38.945][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:38.947][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:38.949][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:38.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:38.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:38.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:38.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:38.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:38.965][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:38.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:38.970][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:38.971][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:38.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.974][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:38.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:38.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.982][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:38.983][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:38.984][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.986][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.988][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:38.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:38.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.994][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:38.995][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:38.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:38.998][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:38.999][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:39.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:39.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.006][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:39.007][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:39.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.010][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.012][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:39.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:39.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.017][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:39.019][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:39.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.022][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:39.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:39.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.030][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:39.031][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:39.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.034][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.035][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:39.037][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:39.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.040][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.041][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:39.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:39.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.062][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:39.064][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:39.065][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.067][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:39.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:39.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.078][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:39.079][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:39.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.082][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.084][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:39.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:39.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.095][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:39.096][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:39.097][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.102][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.105][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:39.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:39.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.111][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:39.119][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:39.121][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.123][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.125][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:39.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:39.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:39.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:39.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.146][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:39.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:39.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:39.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:39.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:39.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:39.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:39.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:39.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:39.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:39.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:39.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:39.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:39.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:39.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:39.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:39.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:39.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:39.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:39.257][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-04-21 19:22:39.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:39.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:39.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:39.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:39.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:39.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:39.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:39.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:39.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:39.295][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:39.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:39.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:39.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:39.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:39.326][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:39.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:39.336][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-04-21 19:22:39.339][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:39.342][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-04-21 19:22:39.346][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:39.347][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:39.356][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:39.358][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:39.360][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:39.361][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:39.372][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:39.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:39.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:39.384][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:39.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:39.387][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:39.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:39.390][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-04-21 19:22:39.405][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:39.407][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:39.409][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-04-21 19:22:39.767][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-04-21 19:22:40.108][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:40.111][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-04-21 19:22:40.117][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-04-21 19:22:40.121][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-04-21 19:22:40.124][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:40.126][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:40.128][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:40.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:40.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:40.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:40.141][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:40.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:40.144][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:40.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:40.149][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:40.151][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:40.152][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.154][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:40.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:40.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.162][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:40.163][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:40.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.166][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.168][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:40.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:40.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.174][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:40.175][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:40.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.178][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.180][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:40.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:40.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.186][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:40.187][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:40.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.190][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.192][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:40.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:40.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.198][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:40.199][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:40.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.215][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.217][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:40.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:40.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.224][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:40.226][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:40.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.229][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.231][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:40.232][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:40.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.235][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.237][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:40.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:40.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.243][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:40.244][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:40.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.247][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:40.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:40.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.254][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:40.256][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:40.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.258][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.260][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:40.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:40.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.266][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:40.268][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:40.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.270][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.272][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:40.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:40.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.278][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:40.280][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:40.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.282][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.284][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:40.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:40.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:40.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:40.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:40.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:40.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:40.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:40.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:40.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:40.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:40.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:40.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:40.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:40.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:40.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:40.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:40.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:40.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:40.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:40.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:40.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:40.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:40.396][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-04-21 19:22:40.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:40.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:40.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.433][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:40.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:40.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:40.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:40.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:40.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:40.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:40.460][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:40.461][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:40.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:40.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:40.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:40.498][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:40.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:40.501][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-04-21 19:22:40.506][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:40.509][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-04-21 19:22:40.511][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:40.513][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:40.514][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:40.516][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:40.524][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:40.525][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:40.529][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:40.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:40.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:40.546][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:40.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:40.549][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:40.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:40.552][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-04-21 19:22:40.563][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:40.564][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:40.566][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-04-21 19:22:40.911][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-04-21 19:22:41.252][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:41.256][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-04-21 19:22:41.261][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-04-21 19:22:41.265][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-04-21 19:22:41.267][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:41.269][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:41.271][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:41.273][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:41.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:41.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:41.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:41.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:41.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:41.288][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[2025-04-21 19:22:41.291][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:41.293][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:41.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.296][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:41.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:41.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.303][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:41.305][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:41.306][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.307][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.309][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:41.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:41.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.314][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:41.316][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:41.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.318][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.333][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:41.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:41.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.341][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:41.342][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:41.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.345][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.347][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:41.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:41.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.353][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:41.354][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:41.355][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.357][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.358][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:41.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:41.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.364][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:41.365][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:41.367][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.368][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.370][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:41.371][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:41.372][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.374][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.375][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:41.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:41.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.381][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:41.382][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:41.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.385][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:41.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:41.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.392][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:41.393][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:41.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.396][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.398][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:41.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:41.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.403][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:41.405][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:41.406][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.407][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.409][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:41.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:41.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.416][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:41.418][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:41.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.421][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.423][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:41.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:41.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:41.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:41.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.443][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:41.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:41.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:41.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:41.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:41.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:41.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:41.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:41.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:41.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:41.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:41.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:41.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:41.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:41.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:41.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:41.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:41.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:41.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:41.565][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-04-21 19:22:41.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:41.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:41.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.579][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:41.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:41.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:41.594][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:41.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:41.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:41.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:41.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:41.604][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:41.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:41.627][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:41.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:41.630][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:41.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:41.633][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-04-21 19:22:41.634][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:41.644][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-04-21 19:22:41.647][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:41.649][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:41.651][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:41.660][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:41.662][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:41.663][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:41.667][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:41.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:41.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:41.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:41.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:41.693][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:41.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:41.697][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-04-21 19:22:41.709][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:41.711][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:41.714][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-04-21 19:22:42.077][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-04-21 19:22:42.424][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:42.428][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-04-21 19:22:42.433][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-04-21 19:22:42.437][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-04-21 19:22:42.440][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:42.442][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:42.444][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:42.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:42.448][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:42.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:42.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:42.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:42.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:42.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:42.464][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:42.465][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:42.467][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.468][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:42.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:42.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.490][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:42.491][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:42.493][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.494][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.496][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:42.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:42.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.502][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:42.503][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:42.505][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.506][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.508][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:42.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:42.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.513][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:42.515][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:42.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.517][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.519][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:42.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:42.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.525][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:42.526][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:42.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.529][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.531][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:42.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:42.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.536][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:42.538][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:42.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.541][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.543][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:42.544][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:42.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.547][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.549][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:42.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:42.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.555][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:42.556][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:42.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.559][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:42.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:42.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.567][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:42.568][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:42.570][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.571][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.573][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:42.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:42.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.579][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:42.581][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:42.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.584][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.586][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:42.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:42.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.592][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:42.593][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:42.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.596][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.598][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:42.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:42.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:42.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:42.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:42.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:42.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:42.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:42.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:42.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:42.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:42.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:42.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:42.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:42.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:42.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:42.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:42.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:42.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:42.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:42.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:42.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:42.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:42.708][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-04-21 19:22:42.718][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:42.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:42.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.725][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:42.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:42.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:42.736][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:42.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:42.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:42.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:42.747][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:42.749][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:42.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:42.759][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:42.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:42.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:42.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:42.766][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-04-21 19:22:42.774][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:42.777][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-04-21 19:22:42.780][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:42.781][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:42.791][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:42.793][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:42.794][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:42.796][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:42.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:42.815][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:42.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:42.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:42.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:42.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:42.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:42.838][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-04-21 19:22:42.850][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:42.852][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:42.854][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-04-21 19:22:43.208][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-04-21 19:22:43.551][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:43.554][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-04-21 19:22:43.560][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-04-21 19:22:43.564][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-04-21 19:22:43.567][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:43.569][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:43.583][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:43.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:43.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:43.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:43.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:43.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:43.601][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:43.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:43.605][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:43.607][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:43.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.610][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:43.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:43.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.617][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:43.618][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:43.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.621][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.623][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:43.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:43.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.628][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:43.630][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:43.631][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.632][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.634][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:43.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:43.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.639][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:43.641][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:43.642][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.644][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.645][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:43.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:43.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.651][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:43.652][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:43.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.655][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.656][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:43.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:43.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.662][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:43.664][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:43.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.667][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.668][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:43.670][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:43.671][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.672][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.674][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:43.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:43.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.680][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:43.681][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:43.683][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.684][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:43.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:43.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.691][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:43.693][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:43.694][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.695][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.697][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:43.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:43.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.703][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:43.704][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:43.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.707][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.709][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:43.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:43.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.714][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:43.733][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:43.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.737][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.739][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:43.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:43.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.749][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:43.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:43.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.754][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:43.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:43.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:43.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:43.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.778][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:43.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:43.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:43.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:43.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:43.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:43.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:43.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:43.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:43.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:43.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:43.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:43.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:43.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:43.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:43.851][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-04-21 19:22:43.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:43.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:43.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:43.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:43.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:43.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:43.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:43.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:43.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:43.915][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 19:22:43.939][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 19:22:43.941][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-21 19:22:43.943][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 19:22:43.945][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-21 19:22:43.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:43.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:43.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:43.974][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:44.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:44.006][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:44.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:44.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.024][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.033][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:44.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:44.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:44.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:44.066][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:44.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:44.069][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:44.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:44.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.086][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.103][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.116][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:44.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:44.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:44.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:44.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:44.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:44.189][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:44.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:44.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.211][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.217][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.223][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:44.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:44.237][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:44.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:44.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:44.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:44.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:44.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:44.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.647][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:44.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:44.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:44.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:44.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:44.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:44.674][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:44.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:44.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.689][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.706][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:44.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:44.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:44.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:44.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:44.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:44.761][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:44.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:44.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.773][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.788][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:44.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:44.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:44.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:44.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:44.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:44.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:44.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:44.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.829][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:44.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:44.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:44.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:44.883][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:44.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:44.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:44.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:44.899][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.942][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:44.949][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:44.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:44.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:44.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:44.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:44.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:44.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:44.977][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:44.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:44.986][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:44.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.001][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:45.016][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:45.017][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:45.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:45.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:45.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:45.041][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:45.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:45.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.065][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:45.084][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:45.092][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:45.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:45.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:45.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:45.132][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:45.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:45.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.151][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:45.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:45.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:45.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:45.193][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:45.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:45.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:45.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:45.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.222][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.231][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:45.246][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:45.248][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:45.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:45.270][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:45.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:45.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:45.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:45.308][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:45.335][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:45.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:45.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:45.349][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:45.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:45.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:45.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:45.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.382][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:45.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:45.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:45.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:45.415][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:45.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:45.418][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:45.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:45.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.493][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:45.503][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:45.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:45.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:45.522][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:45.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:45.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:45.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:45.530][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:45.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:45.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:45.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:45.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:45.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:45.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:45.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:45.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.634][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.650][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:45.681][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:45.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:45.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:45.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:45.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:45.699][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:45.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:45.714][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.748][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:45.755][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:45.757][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:45.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:45.768][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:45.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:45.772][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:45.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:45.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.817][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:45.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:45.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:45.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:45.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:45.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:45.884][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:45.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:45.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:45.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:45.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:45.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:45.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:45.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:45.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:45.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:45.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:45.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:46.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:46.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:46.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:46.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:46.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:46.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:46.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:46.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:46.099][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 19:22:46.116][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:46.117][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:46.120][private$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[2025-04-21 19:22:46.483][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[2025-04-21 19:22:46.824][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:46.827][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-04-21 19:22:46.833][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-04-21 19:22:46.839][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[2025-04-21 19:22:46.843][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:46.845][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:46.847][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-21 19:22:47.193][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-21 19:22:47.531][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:47.534][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-04-21 19:22:47.540][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-04-21 19:22:47.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:47.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:47.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:47.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:47.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:47.558][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:47.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:47.561][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-04-21 19:22:47.562][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:47.565][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-04-21 19:22:47.566][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:47.568][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:47.570][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:47.571][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:47.572][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:47.574][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:47.578][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:47.579][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:47.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:47.588][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:47.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:47.591][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:47.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:47.594][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-04-21 19:22:47.598][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:47.600][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:47.602][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-04-21 19:22:47.938][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-04-21 19:22:48.289][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:48.292][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-04-21 19:22:48.298][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-04-21 19:22:48.303][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-04-21 19:22:48.305][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:48.307][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:48.309][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:48.312][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:48.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:48.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:48.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:48.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:48.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:48.327][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[2025-04-21 19:22:48.330][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:48.331][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:48.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.334][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:48.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:48.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.341][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:48.343][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:48.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.345][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.347][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:48.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:48.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.360][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:48.362][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:48.364][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.365][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.368][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:48.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:48.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.373][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:48.375][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:48.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.377][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.379][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:48.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:48.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.385][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:48.386][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:48.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.388][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.390][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:48.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:48.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.396][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:48.397][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:48.398][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.399][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.401][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:48.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:48.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.407][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:48.408][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:48.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.411][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.413][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:48.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:48.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.418][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:48.421][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:48.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.425][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:48.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:48.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.433][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:48.434][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:48.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.436][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.440][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:48.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:48.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.451][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:48.452][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:48.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.455][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.457][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:48.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:48.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.462][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:48.464][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:48.465][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.466][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.468][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:48.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:48.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:48.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:48.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:48.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:48.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:48.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:48.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:48.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:48.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:48.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:48.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:48.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:48.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:48.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:48.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:48.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:48.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:48.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:48.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:48.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:48.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:48.545][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-04-21 19:22:48.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:48.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:48.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:48.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:48.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:48.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:48.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:48.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:48.570][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:48.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:48.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:48.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:48.590][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:48.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:48.593][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:48.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:48.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:48.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:48.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:48.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:48.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:48.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:48.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:48.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:48.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:48.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:48.650][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:48.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:48.653][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:48.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:48.656][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-04-21 19:22:48.666][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:22:48.697][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-04-21 19:22:48.699][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:22:48.700][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:22:48.708][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:22:48.710][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:22:48.711][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:22:48.712][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:22:48.716][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:48.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:48.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:48.747][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:48.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:48.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:48.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:48.753][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-04-21 19:22:48.761][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:48.764][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:48.766][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-04-21 19:22:49.113][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-04-21 19:22:49.462][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:49.465][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-04-21 19:22:49.470][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-04-21 19:22:49.475][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-04-21 19:22:49.477][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:22:49.479][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:22:49.481][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:22:49.483][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:49.484][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:49.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:49.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:49.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:49.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:49.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:49.502][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:49.503][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:49.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.506][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:49.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:49.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.513][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:49.514][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:49.515][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.516][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.518][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:22:49.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:22:49.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.523][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:49.525][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:49.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.527][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.529][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:22:49.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:22:49.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.538][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:49.540][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:49.541][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.542][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:22:49.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:22:49.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.550][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:49.551][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:49.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.556][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.560][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:22:49.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:22:49.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.568][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:49.570][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:22:49.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.573][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.574][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:49.576][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:49.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.578][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.580][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:22:49.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:49.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.586][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:49.587][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:49.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.590][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.591][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:49.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:49.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.597][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:49.598][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:49.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.601][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.603][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:22:49.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:22:49.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.608][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:49.610][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:49.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.612][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.614][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:22:49.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:22:49.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.620][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:49.622][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:49.623][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.624][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.626][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:22:49.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:22:49.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:49.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:49.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:49.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:49.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:49.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:49.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.649][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:49.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:49.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:49.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:49.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:49.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:49.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:49.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:49.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:49.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:49.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:49.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:49.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:22:49.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:22:49.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:49.717][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-04-21 19:22:49.721][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:49.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:49.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:49.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:49.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:49.750][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:49.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:49.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:49.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:49.804][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 19:22:49.843][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:49.845][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:49.849][private$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[2025-04-21 19:22:50.290][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[2025-04-21 19:22:50.700][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2025-04-21 19:22:50.703][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-04-21 19:22:50.706][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-04-21 19:22:50.714][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-04-21 19:22:50.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:50.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:50.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:50.733][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:50.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:50.737][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:50.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:50.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:50.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:50.755][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:50.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:50.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:50.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:50.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:50.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:50.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:50.785][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:50.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:50.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:50.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:50.793][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:50.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:50.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:50.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:50.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:50.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:50.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:50.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:50.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:50.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:50.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:50.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:50.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:50.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:50.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:50.847][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:50.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:50.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:50.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:50.858][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:50.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:50.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:50.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:50.874][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:50.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:50.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:50.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:50.887][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:50.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:50.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:50.900][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:50.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:50.903][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:50.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:50.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:50.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:50.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:50.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:50.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:50.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:50.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:50.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:50.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:50.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:50.948][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:50.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:50.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:50.960][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:50.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:50.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:50.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:50.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:50.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:50.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:50.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:51.058][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:51.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:51.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:51.075][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:51.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:51.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:51.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:51.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:51.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:51.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:51.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:51.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:51.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:51.164][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:51.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:51.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:51.226][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:51.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:51.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:51.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:51.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:51.256][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:51.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:51.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.278][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:51.318][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:51.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:51.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:51.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:51.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:51.337][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:51.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:51.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:51.400][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:51.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:51.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:51.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:51.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:51.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:51.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:51.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:51.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:51.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:51.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:51.509][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:51.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:51.526][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:51.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:51.533][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:51.570][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:51.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:51.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:51.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:51.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:51.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:51.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:51.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:51.658][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:51.660][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:51.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:51.698][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:51.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:51.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:51.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:51.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:51.735][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:51.737][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:51.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:51.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:51.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:51.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:51.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:51.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:51.793][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:51.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:51.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:51.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:51.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:51.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:51.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:51.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:51.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:51.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:51.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:51.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:51.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:51.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:51.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:51.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:51.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:51.876][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:51.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:51.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:51.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:51.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:51.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:51.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:51.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:51.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:51.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:51.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:51.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:51.969][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:51.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:51.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:51.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:51.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:51.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:52.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:52.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:52.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:52.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:52.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:52.053][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:52.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:52.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.085][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.097][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:52.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:52.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:52.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:52.134][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:52.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:52.138][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:52.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:52.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.147][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:52.235][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 19:22:52.250][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 19:22:52.252][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-21 19:22:52.254][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 19:22:52.263][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-21 19:22:52.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:52.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:52.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:52.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:52.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:52.285][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:52.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:52.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:52.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:52.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:52.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:52.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:52.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:52.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:52.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:52.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:52.436][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:52.437][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:52.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:52.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:52.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:52.484][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:52.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:52.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.522][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:52.532][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:52.533][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:52.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:52.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:52.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:52.545][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:52.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:52.548][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:52.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:52.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:52.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:52.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:52.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:52.639][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:52.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:52.642][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:52.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:52.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:52.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:52.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:52.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:52.700][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:52.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:52.705][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.710][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.744][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:52.767][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:52.769][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:52.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:52.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:52.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:52.787][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:52.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:52.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:52.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:52.832][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:52.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:52.851][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:52.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:52.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:52.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:52.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:52.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:52.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:52.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:52.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:52.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:52.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:52.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:52.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:52.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:52.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:52.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:52.974][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:52.977][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:52.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:52.988][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:52.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:52.992][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:52.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:52.995][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.017][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.028][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:53.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:53.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:53.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:53.052][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:53.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:53.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:53.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:53.057][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:53.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:53.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:53.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:53.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:53.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:53.096][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:53.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:53.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:53.157][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:53.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:53.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:53.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:53.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:53.171][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:53.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:53.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.196][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:53.247][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:53.252][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:53.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:53.264][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:53.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:53.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:53.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:53.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.277][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.307][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:53.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:53.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:53.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:53.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:53.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:53.351][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:53.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:53.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.397][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:53.403][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:53.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:53.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:53.423][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:53.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:53.426][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:53.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:53.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:53.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:53.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:53.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:53.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:53.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:53.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:53.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:53.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.507][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:53.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:53.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:53.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:53.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:53.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:53.539][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:53.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:53.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:53.600][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:53.601][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:53.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:53.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:53.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:53.619][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:53.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:53.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.645][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:53.658][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:53.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:53.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:53.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:53.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:53.702][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:53.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:53.707][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:53.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.781][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-21 19:22:53.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-21 19:22:53.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-21 19:22:53.807][biodb::testThat]
biodb.INFO [2025-04-21 19:22:53.809][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-04-21 19:22:53.811][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:22:53.815][biodb::testThat]
biodb.TRACE[2025-04-21 19:22:53.825][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-21 19:22:53.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-21 19:22:53.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.831][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:53.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:53.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:53.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:53.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.843][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:53.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:53.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:53.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:53.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:53.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:53.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:53.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:53.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:53.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:53.921][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:53.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:53.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:53.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:53.949][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 19:22:53.970][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:53.973][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:53.977][private$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[2025-04-21 19:22:54.318][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[2025-04-21 19:22:54.659][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:54.663][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-04-21 19:22:54.674][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-04-21 19:22:54.679][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:54.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:54.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:54.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:54.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:54.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:54.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:54.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:54.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:54.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:54.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:54.706][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:54.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:54.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:54.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:54.712][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:54.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:54.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:54.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:54.719][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[2025-04-21 19:22:54.723][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:54.725][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:54.728][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-21 19:22:55.211][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-21 19:22:55.550][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:55.555][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-04-21 19:22:55.563][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-04-21 19:22:55.570][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:55.573][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:55.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:55.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:55.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:55.591][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:55.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:55.596][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:55.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:55.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:55.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:55.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:55.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:55.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:55.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:55.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:55.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:55.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:55.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:55.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:55.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:55.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:55.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:55.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:55.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:55.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:55.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:55.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:55.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:55.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:55.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:55.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:55.684][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-21 19:22:55.686][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:55.688][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:55.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:55.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:55.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:55.700][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:55.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:55.703][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:55.709][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:55.714][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:55.715][private$selectFields]
biodb.TRACE[2025-04-21 19:22:55.717][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 19:22:55.718][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 19:22:55.719][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:55.721][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.722][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.723][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.725][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:55.726][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.727][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.730][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:55.731][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:55.732][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:55.734][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.735][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.736][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.738][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:55.739][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 19:22:55.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:55.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:55.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:55.770][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-04-21 19:22:55.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:55.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:55.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:55.809][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:55.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:55.815][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:55.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:55.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:55.829][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:55.841][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:55.862][private$selectFields]
biodb.TRACE[2025-04-21 19:22:55.864][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 19:22:55.912][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 19:22:55.914][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:55.915][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.930][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.937][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:55.938][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.940][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.943][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:55.944][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:55.946][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:55.947][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.948][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.951][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:55.953][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 19:22:55.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:55.959][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:55.964][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:55.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:55.970][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-21 19:22:55.972][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:55.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:55.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:55.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:55.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:55.985][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:55.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:55.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:55.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:56.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:56.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:56.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:56.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:56.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:56.007][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:56.008][private$selectFields]
biodb.TRACE[2025-04-21 19:22:56.016][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 19:22:56.017][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 19:22:56.019][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:56.021][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:56.022][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:56.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:56.033][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:56.035][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:56.037][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:56.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:56.040][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:56.042][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:56.049][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:56.050][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:56.053][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:56.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:56.055][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:56.057][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 19:22:56.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:56.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:56.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:56.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:56.071][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:56.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:56.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:56.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:56.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:56.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:56.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:56.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:56.091][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-04-21 19:22:56.092][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-21 19:22:56.094][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-21 19:22:56.109][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:56.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:56.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:56.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:56.116][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:56.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:56.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:56.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:56.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:56.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:56.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:56.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:56.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:56.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:56.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:56.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:56.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:56.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:56.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:56.356][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:56.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:56.359][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:56.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:56.381][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 19:22:56.396][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:56.398][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:56.401][private$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[2025-04-21 19:22:56.773][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[2025-04-21 19:22:57.109][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:57.112][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-04-21 19:22:57.118][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-04-21 19:22:57.124][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[2025-04-21 19:22:57.131][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:57.132][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:57.135][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-21 19:22:57.473][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-21 19:22:57.812][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:57.815][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-04-21 19:22:57.822][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-04-21 19:22:57.826][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:57.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:57.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:57.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:57.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:57.840][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:57.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:57.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:57.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:57.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:57.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:57.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:57.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:57.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:57.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:57.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:57.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:57.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:57.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:57.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:57.869][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:57.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:57.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:57.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:57.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:57.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:57.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:57.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:57.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:57.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:57.897][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:57.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:57.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:57.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:57.902][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:57.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:57.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:57.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:57.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:57.909][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:57.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:57.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:57.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:57.922][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:57.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:57.924][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:57.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:57.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:57.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:57.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:57.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:57.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:57.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:57.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:57.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:22:57.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:57.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:57.976][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-21 19:22:58.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:58.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:58.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:58.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:58.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:58.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:58.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:58.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.091][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:58.109][private$selectFields]
biodb.TRACE[2025-04-21 19:22:58.111][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 19:22:58.122][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 19:22:58.123][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:58.125][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.126][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.129][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.131][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.140][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.143][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.145][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:58.146][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:58.147][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.149][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.152][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.153][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 19:22:58.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.185][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-04-21 19:22:58.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:58.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:58.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:58.204][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:58.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:58.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:58.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:58.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.361][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:58.362][private$selectFields]
biodb.TRACE[2025-04-21 19:22:58.372][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 19:22:58.373][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 19:22:58.376][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:58.380][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.382][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.385][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.386][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.388][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.389][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.399][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.401][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:58.425][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:58.426][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.428][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.429][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.431][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.432][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 19:22:58.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.473][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-21 19:22:58.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:58.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:58.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:58.509][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:58.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:58.512][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:58.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:58.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.534][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:58.535][private$selectFields]
biodb.TRACE[2025-04-21 19:22:58.536][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 19:22:58.538][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 19:22:58.539][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:58.564][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.572][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.575][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.577][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.579][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.580][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.590][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.592][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:58.594][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:22:58.596][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.597][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.600][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.621][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 19:22:58.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:22:58.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.650][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-04-21 19:22:58.658][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-21 19:22:58.660][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-21 19:22:58.683][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-21 19:22:58.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-21 19:22:58.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-21 19:22:58.726][biodb::testThat]
biodb.INFO [2025-04-21 19:22:58.728][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-04-21 19:22:58.733][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:22:58.739][biodb::testThat]
biodb.TRACE[2025-04-21 19:22:58.749][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-21 19:22:58.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-21 19:22:58.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.758][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:58.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:58.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.764][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:58.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:58.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:58.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:58.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:58.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:58.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:58.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:58.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:58.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:58.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:58.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:58.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:58.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:58.809][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:58.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:22:58.815][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.INFO [2025-04-21 19:22:58.819][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2025-04-21 19:22:58.821][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:58.823][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:58.825][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-21 19:22:59.162][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-21 19:22:59.499][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:22:59.501][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-04-21 19:22:59.507][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-04-21 19:22:59.510][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:22:59.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:22:59.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:22:59.520][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:22:59.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:22:59.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:22:59.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:22:59.526][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:59.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:59.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:59.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:59.531][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:59.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:59.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:59.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:22:59.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:59.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:22:59.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:22:59.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:22:59.542][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 19:22:59.546][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:22:59.547][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:22:59.550][private$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[2025-04-21 19:22:59.885][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[2025-04-21 19:23:00.220][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:23:00.223][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-04-21 19:23:00.253][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-04-21 19:23:00.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:00.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:00.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:00.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:00.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:00.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:00.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:00.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:00.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:00.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.306][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:00.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:00.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:00.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:00.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:23:00.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:00.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:00.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:00.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:00.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:00.328][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:00.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:00.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:00.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:00.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:00.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:00.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:00.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:00.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:23:00.344][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-21 19:23:00.346][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:00.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:00.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:00.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:00.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:00.358][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:00.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:00.361][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.371][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:00.372][private$selectFields]
biodb.TRACE[2025-04-21 19:23:00.373][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 19:23:00.375][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 19:23:00.376][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:00.377][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.378][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.380][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.382][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.383][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.384][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.386][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.387][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:00.388][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:00.388][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.389][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.391][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.392][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.393][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 19:23:00.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.408][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-04-21 19:23:00.409][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:00.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:00.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:00.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:00.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:00.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:00.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:00.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.434][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:00.435][private$selectFields]
biodb.TRACE[2025-04-21 19:23:00.436][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 19:23:00.437][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 19:23:00.439][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:00.440][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.441][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.443][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.444][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.445][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.447][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.449][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.450][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:00.452][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:00.453][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.455][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.457][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.458][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 19:23:00.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.476][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-21 19:23:00.477][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:00.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:00.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:00.487][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:00.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:00.489][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:00.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:00.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.503][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:00.504][private$selectFields]
biodb.TRACE[2025-04-21 19:23:00.505][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 19:23:00.506][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 19:23:00.506][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:00.508][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.510][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.511][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.512][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.513][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.515][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.517][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.519][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:00.520][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:00.521][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.523][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.525][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.526][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 19:23:00.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:00.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.550][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-04-21 19:23:00.553][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-21 19:23:00.554][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-21 19:23:00.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:00.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:00.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:00.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:00.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:00.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:00.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:00.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:00.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:00.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:00.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:23:00.596][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:00.598][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:00.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:00.607][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:00.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:00.609][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:00.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:00.614][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[2025-04-21 19:23:00.619][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:23:00.620][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:23:00.623][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-21 19:23:00.959][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-21 19:23:01.306][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:23:01.311][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-04-21 19:23:01.319][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-04-21 19:23:01.326][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-21 19:23:01.333][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:23:01.337][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:23:01.340][private$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[2025-04-21 19:23:01.691][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[2025-04-21 19:23:02.028][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:23:02.032][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-04-21 19:23:02.038][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-04-21 19:23:02.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:02.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:02.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:02.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:02.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:02.056][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:02.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:02.059][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:02.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:02.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:02.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:02.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:02.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:02.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:23:02.081][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:02.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:02.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:02.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:02.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:02.096][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:02.097][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[2025-04-21 19:23:02.098][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:02.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:02.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:02.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:02.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.109][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:02.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:02.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:23:02.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:02.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:02.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:02.124][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:02.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:02.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:02.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:02.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:02.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:02.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.134][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:02.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:02.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.140][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:02.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:02.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:23:02.145][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-21 19:23:02.147][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:02.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:02.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:02.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:02.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:02.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:02.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:02.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.169][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.191][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:02.192][private$selectFields]
biodb.TRACE[2025-04-21 19:23:02.193][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 19:23:02.194][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 19:23:02.196][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:02.197][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.198][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.200][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.201][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.202][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.204][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.205][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.206][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:02.208][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:02.209][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.210][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.212][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.214][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 19:23:02.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.225][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.230][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-04-21 19:23:02.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:02.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:02.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:02.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:02.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:02.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:02.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:02.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.255][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:02.256][private$selectFields]
biodb.TRACE[2025-04-21 19:23:02.257][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 19:23:02.258][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 19:23:02.259][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:02.261][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.262][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.265][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.266][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.267][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.269][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.270][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:02.271][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:02.272][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.274][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.275][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.276][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.278][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 19:23:02.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.292][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-21 19:23:02.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:02.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:02.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:02.303][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:02.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:02.306][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:02.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:02.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.329][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:02.330][private$selectFields]
biodb.TRACE[2025-04-21 19:23:02.332][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 19:23:02.333][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 19:23:02.334][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:02.336][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.340][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.344][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.346][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.347][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.352][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.353][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:02.355][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:02.357][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.358][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.361][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.364][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 19:23:02.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.389][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-04-21 19:23:02.390][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-21 19:23:02.392][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-21 19:23:02.437][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-21 19:23:02.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-21 19:23:02.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-21 19:23:02.448][biodb::testThat]
biodb.INFO [2025-04-21 19:23:02.449][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-04-21 19:23:02.451][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:23:02.452][biodb::testThat]
biodb.TRACE[2025-04-21 19:23:02.464][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-21 19:23:02.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-21 19:23:02.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.470][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.497][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:23:02.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:02.550][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:02.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:02.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:02.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:02.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:02.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:02.574][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[2025-04-21 19:23:02.579][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 19:23:02.581][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-04-21 19:23:02.583][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 19:23:02.597][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-04-21 19:23:02.600][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:02.601][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:02.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:02.626][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:02.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:02.629][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:02.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:02.632][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.647][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.662][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:23:02.669][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[2025-04-21 19:23:02.679][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 19:23:02.681][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-04-21 19:23:02.684][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 19:23:02.686][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-04-21 19:23:02.697][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:02.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:02.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:02.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:02.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:02.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:02.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:02.714][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:23:02.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:02.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:02.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:02.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:02.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:02.783][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:02.785][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.TRACE[2025-04-21 19:23:02.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:02.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:23:02.819][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-21 19:23:02.829][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:02.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:02.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:02.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:02.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:02.853][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:02.854][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.TRACE[2025-04-21 19:23:02.856][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.887][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:02.889][private$selectFields]
biodb.TRACE[2025-04-21 19:23:02.890][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 19:23:02.892][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 19:23:02.893][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:02.895][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.903][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.906][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.907][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.909][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.912][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.922][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:02.924][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:02.925][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.926][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.929][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.937][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 19:23:02.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:02.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:02.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:02.978][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-04-21 19:23:02.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:02.981][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:02.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:02.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:02.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:02.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:02.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:02.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.014][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.042][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:03.043][private$selectFields]
biodb.TRACE[2025-04-21 19:23:03.045][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 19:23:03.046][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 19:23:03.047][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:03.049][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.050][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.060][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.061][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.063][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.065][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.067][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:03.074][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:03.076][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.077][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.080][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.082][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 19:23:03.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.107][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.115][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-21 19:23:03.124][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:03.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:03.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:03.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:03.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:03.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:03.147][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[2025-04-21 19:23:03.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.174][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:03.176][private$selectFields]
biodb.TRACE[2025-04-21 19:23:03.177][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 19:23:03.202][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 19:23:03.203][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:03.205][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.207][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.210][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.211][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.213][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.215][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.217][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:03.218][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:03.219][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.221][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.223][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.225][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 19:23:03.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.263][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-04-21 19:23:03.265][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-21 19:23:03.266][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-21 19:23:03.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.350][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.357][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:23:03.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:03.409][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:03.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:03.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:03.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:03.433][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:03.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:03.448][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[2025-04-21 19:23:03.453][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 19:23:03.463][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-04-21 19:23:03.465][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 19:23:03.468][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-04-21 19:23:03.485][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[2025-04-21 19:23:03.501][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 19:23:03.505][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-04-21 19:23:03.509][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 19:23:03.519][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-04-21 19:23:03.524][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:03.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:03.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:03.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:03.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:03.553][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:03.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:03.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.569][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.585][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:23:03.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:03.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:03.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:03.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:03.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:03.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:03.619][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[2025-04-21 19:23:03.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.638][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.645][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:23:03.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:03.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:03.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:03.701][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:03.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:03.704][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:03.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:03.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:03.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:23:03.758][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-21 19:23:03.769][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:03.770][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:03.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:03.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:03.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:03.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:03.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:03.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.823][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:03.824][private$selectFields]
biodb.TRACE[2025-04-21 19:23:03.833][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 19:23:03.834][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 19:23:03.836][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:03.837][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.839][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.841][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.842][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.851][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.852][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.854][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.856][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:03.857][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:03.859][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.866][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.868][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.869][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.871][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 19:23:03.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.906][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-04-21 19:23:03.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:03.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:03.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:03.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:03.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:03.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:03.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:03.949][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:03.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:03.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:03.989][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:03.991][private$selectFields]
biodb.TRACE[2025-04-21 19:23:03.996][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 19:23:04.000][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 19:23:04.003][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:04.004][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.006][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:04.009][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:04.015][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.018][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:04.023][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:04.024][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:04.026][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:04.031][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.033][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:04.036][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:04.037][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 19:23:04.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:04.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:04.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:04.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:04.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:04.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:04.075][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-21 19:23:04.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:04.092][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:04.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:04.124][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:04.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:04.127][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:04.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:04.130][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:04.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:04.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:04.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:04.158][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:04.160][private$selectFields]
biodb.TRACE[2025-04-21 19:23:04.161][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-21 19:23:04.163][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-21 19:23:04.171][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:04.173][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.176][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:04.188][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:04.189][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.191][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:04.193][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:04.195][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:04.196][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-21 19:23:04.198][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.199][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:04.201][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:04.225][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-21 19:23:04.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:04.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:04.242][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:04.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:04.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:04.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:04.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:04.254][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-04-21 19:23:04.263][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-21 19:23:04.264][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-21 19:23:04.305][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-21 19:23:04.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-21 19:23:04.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:04.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-21 19:23:04.354][biodb::testThat]
biodb.INFO [2025-04-21 19:23:04.356][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-04-21 19:23:04.357][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:23:04.359][biodb::testThat]
biodb.DEBUG[2025-04-21 19:23:04.361][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-04-21 19:23:04.367][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:23:04.369][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-04-21 19:23:04.371][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:23:04.382][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:23:04.386][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:23:04.388][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:23:04.390][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:23:04.391][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:23:04.400][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:04.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:04.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:04.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:04.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:04.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:04.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:04.416][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-04-21 19:23:04.428][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:23:04.429][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:23:04.432][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-04-21 19:23:04.793][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-04-21 19:23:05.133][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:23:05.136][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-04-21 19:23:05.142][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-04-21 19:23:05.146][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-04-21 19:23:05.149][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:23:05.151][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:23:05.153][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:23:05.155][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:05.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:05.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:05.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:05.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:05.168][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:05.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:05.172][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:05.174][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:05.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.177][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:05.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:05.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:05.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:05.184][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:23:05.185][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:23:05.186][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.188][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:05.189][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:23:05.191][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:23:05.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.193][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:05.195][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:23:05.197][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:23:05.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.199][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:05.201][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:23:05.202][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:23:05.213][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.215][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:05.217][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:23:05.218][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:23:05.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.221][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:05.223][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:23:05.225][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:05.226][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.227][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:05.233][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:05.235][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:05.237][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.239][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:05.241][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:23:05.242][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:23:05.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.245][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:05.247][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:23:05.248][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:23:05.250][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.251][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:05.253][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:23:05.254][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:23:05.256][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.257][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:05.259][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:05.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:05.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:05.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:05.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:05.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:05.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:05.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:05.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:05.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:05.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:05.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:05.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:05.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:05.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:05.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:05.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:05.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:05.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:05.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:05.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:05.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:05.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:05.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:05.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:05.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:05.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:05.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:05.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:05.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:05.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:23:05.328][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-04-21 19:23:05.329][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-04-21 19:23:05.343][biodb::testThat]
biodb.INFO [2025-04-21 19:23:05.344][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-04-21 19:23:05.346][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:23:05.347][biodb::testThat]
biodb.DEBUG[2025-04-21 19:23:05.361][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-04-21 19:23:05.363][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-04-21 19:23:05.365][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-04-21 19:23:05.376][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-04-21 19:23:05.387][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-04-21 19:23:05.389][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:23:05.391][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:23:05.393][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:23:05.396][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:23:05.398][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:23:05.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:05.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:05.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:05.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:05.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:05.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:05.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:05.448][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-04-21 19:23:05.468][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:23:05.480][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:23:05.482][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-04-21 19:23:05.822][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-04-21 19:23:06.171][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:23:06.175][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-04-21 19:23:06.182][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-04-21 19:23:06.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:06.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:06.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:06.200][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:06.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:06.204][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:06.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:06.216][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-04-21 19:23:06.222][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:23:06.225][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:23:06.228][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-04-21 19:23:06.569][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-04-21 19:23:06.906][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:23:06.908][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-04-21 19:23:06.915][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-04-21 19:23:06.917][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:06.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:06.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:06.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:06.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:06.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:06.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:06.933][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-04-21 19:23:06.936][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:23:06.937][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:23:06.939][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-04-21 19:23:07.279][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-04-21 19:23:07.623][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:23:07.629][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-04-21 19:23:07.635][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-04-21 19:23:07.639][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-04-21 19:23:07.651][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:23:07.655][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-04-21 19:23:07.657][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-04-21 19:23:07.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:07.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:07.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:07.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:07.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:07.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:07.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:07.678][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:07.679][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:07.680][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.682][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:07.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:07.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.689][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:23:07.690][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:23:07.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.693][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.694][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:23:07.696][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:23:07.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.698][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.700][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:23:07.707][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:23:07.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.710][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.712][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:23:07.713][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:23:07.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.716][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.749][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:23:07.751][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:23:07.753][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.754][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.756][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:23:07.758][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:07.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.760][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.762][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:07.763][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:07.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.766][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.768][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:23:07.769][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:23:07.770][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.772][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.774][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:23:07.775][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:23:07.776][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.778][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.779][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:23:07.781][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:23:07.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.783][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.785][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:07.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:07.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:07.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:07.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:07.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:07.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:07.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:07.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:07.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:07.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:07.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:07.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:07.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:07.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:23:07.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:07.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:07.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:07.854][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:07.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:07.856][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:07.858][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[2025-04-21 19:23:07.861][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:07.862][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:07.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.865][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:07.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:07.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.872][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:23:07.884][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:23:07.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.888][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.889][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:23:07.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:23:07.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.903][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:23:07.911][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:23:07.913][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.916][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.919][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:23:07.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:23:07.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.933][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:23:07.935][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:23:07.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.939][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.942][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:23:07.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:23:07.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.949][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:23:07.950][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:23:07.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.952][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.953][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:23:07.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:23:07.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.970][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:23:07.971][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:23:07.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.980][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.985][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:23:07.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:23:07.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.993][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:23:07.995][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:07.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:07.998][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:07.999][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:23:08.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:08.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.007][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:08.009][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:08.012][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.013][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:08.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:08.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.025][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:23:08.026][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:23:08.028][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.030][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.032][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:23:08.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:23:08.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.045][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:23:08.046][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:23:08.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.049][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.052][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:23:08.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:23:08.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.066][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:23:08.068][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:23:08.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.070][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.073][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:23:08.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:23:08.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:08.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:08.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:08.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:08.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:08.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:08.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:08.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:08.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:08.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:08.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:08.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:08.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:08.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:08.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:23:08.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:08.123][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:08.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:08.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:08.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:08.136][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:08.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:08.141][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:08.142][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:08.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.145][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:08.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:08.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.151][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:23:08.152][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:23:08.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.155][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.157][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:23:08.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:23:08.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.161][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:23:08.162][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:23:08.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.164][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.165][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:23:08.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:23:08.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.170][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:23:08.171][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:23:08.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.172][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.174][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:23:08.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:23:08.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.177][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:23:08.178][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:23:08.179][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.180][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.197][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:23:08.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:23:08.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.206][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:23:08.209][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:23:08.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.211][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.213][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:23:08.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:23:08.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.216][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:23:08.219][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:08.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.221][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.223][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:23:08.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:08.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.229][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:08.230][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:08.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.233][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:08.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:08.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.241][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:23:08.242][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:23:08.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.244][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.245][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:23:08.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:23:08.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.249][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:23:08.250][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:23:08.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.253][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.254][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:23:08.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:23:08.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.272][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:23:08.274][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:23:08.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.295][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.297][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:23:08.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:23:08.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:08.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:08.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:08.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:08.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:08.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:08.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.331][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:08.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:08.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:08.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:08.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:08.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:08.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:08.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:08.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:08.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:08.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:08.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:08.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:08.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:08.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:08.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:08.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:08.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:08.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:08.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:08.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:08.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:08.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:08.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:08.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:08.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:08.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:08.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:08.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:23:08.473][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-04-21 19:23:08.478][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-04-21 19:23:08.484][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-04-21 19:23:08.542][biodb::testThat]
biodb.INFO [2025-04-21 19:23:08.544][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-04-21 19:23:08.545][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:23:08.546][biodb::testThat]
biodb.INFO [2025-04-21 19:23:08.601][biodb::testThat]
biodb.INFO [2025-04-21 19:23:08.602][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-04-21 19:23:08.603][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:23:08.604][biodb::testThat]
biodb.INFO [2025-04-21 19:23:08.624][biodb::testThat]
biodb.INFO [2025-04-21 19:23:08.625][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-04-21 19:23:08.626][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:23:08.627][biodb::testThat]
biodb.DEBUG[2025-04-21 19:23:08.631][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[2025-04-21 19:23:08.636][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:23:08.637][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:23:08.641][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-04-21 19:23:09.013][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-04-21 19:23:09.472][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:23:09.476][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-04-21 19:23:09.483][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-04-21 19:23:09.503][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:23:09.505][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:23:09.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:09.508][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:09.510][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:09.516][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:09.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:09.519][ef$get] fields variable is a list.
biodb.INFO [2025-04-21 19:23:09.526][biodb::testThat]
biodb.INFO [2025-04-21 19:23:09.528][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2025-04-21 19:23:09.530][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:23:09.531][biodb::testThat]
biodb.ERROR[2025-04-21 19:23:09.556][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-04-21 19:23:09.580][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-04-21 19:23:09.619][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-21 19:23:09.621][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-21 19:23:09.624][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-21 19:23:09.625][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-21 19:23:09.627][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:09.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:09.630][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:09.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:09.634][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:09.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-21 19:23:09.664][biodb::testContext]
biodb.INFO [2025-04-21 19:23:09.665][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-21 19:23:09.667][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-04-21 19:23:09.669][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-21 19:23:09.670][biodb::testContext]
biodb.INFO [2025-04-21 19:23:09.674][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-21 19:23:09.694][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-21 19:23:09.704][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 19:23:09.717][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-21 19:23:09.718][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-21 19:23:09.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:09.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:09.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:09.724][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-21 19:23:09.725][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-21 19:23:09.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:09.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:09.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:09.729][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-21 19:23:09.730][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-21 19:23:09.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:09.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:09.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:09.735][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-21 19:23:09.737][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-21 19:23:09.738][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-21 19:23:09.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:09.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:09.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:09.744][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-21 19:23:09.745][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-21 19:23:09.747][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-21 19:23:09.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:09.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:09.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:09.753][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-21 19:23:09.754][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-21 19:23:09.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:09.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:09.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:09.760][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-21 19:23:09.761][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-21 19:23:09.763][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-21 19:23:09.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:09.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:09.767][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[2025-04-21 19:23:09.768][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-21 19:23:09.770][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-21 19:23:09.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:09.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:09.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:09.775][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-21 19:23:09.776][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-21 19:23:09.777][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-21 19:23:09.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:09.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:09.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:09.782][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-21 19:23:09.783][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-21 19:23:09.785][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-21 19:23:09.786][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-21 19:23:09.788][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-21 19:23:09.789][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-21 19:23:09.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:09.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:09.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:09.795][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-21 19:23:09.797][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-21 19:23:09.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:09.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:09.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:09.802][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-21 19:23:09.803][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-21 19:23:09.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:09.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:09.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:09.808][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-21 19:23:09.809][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-21 19:23:09.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:09.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:09.813][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[2025-04-21 19:23:09.814][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-21 19:23:09.816][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-21 19:23:09.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:09.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:09.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:09.821][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-21 19:23:09.823][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-21 19:23:09.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:09.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:09.827][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[2025-04-21 19:23:09.839][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-21 19:23:09.851][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-21 19:23:10.007][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-21 19:23:10.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.013][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-21 19:23:10.015][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-21 19:23:10.017][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-21 19:23:10.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.021][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[2025-04-21 19:23:10.022][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-21 19:23:10.025][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:10.026][self$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[2025-04-21 19:23:10.028][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:10.029][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 19:23:10.031][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:10.040][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 19:23:10.042][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:10.044][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 19:23:10.046][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-21 19:23:10.048][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 19:23:10.049][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:10.051][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-21 19:23:10.052][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 19:23:10.054][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:10.055][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:10.057][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 19:23:10.057][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 19:23:10.057][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 19:23:10.057][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-21 19:23:10.057][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-21 19:23:10.059][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 19:23:10.060][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:10.062][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:10.063][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 19:23:10.064][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:10.066][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:10.067][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 19:23:10.068][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:10.070][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 19:23:10.071][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 19:23:10.073][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:10.075][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:10.076][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-21 19:23:10.079][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:10.080][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-21 19:23:10.082][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:10.083][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 19:23:10.084][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:10.086][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 19:23:10.087][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:10.089][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 19:23:10.090][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-21 19:23:10.092][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 19:23:10.093][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:10.094][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-21 19:23:10.096][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 19:23:10.097][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:10.099][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:10.100][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 19:23:10.100][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 19:23:10.100][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 19:23:10.100][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-21 19:23:10.100][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-21 19:23:10.102][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 19:23:10.103][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:10.104][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:10.106][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 19:23:10.108][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:10.109][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:10.110][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 19:23:10.112][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:10.113][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 19:23:10.114][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 19:23:10.116][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:10.118][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:10.119][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-21 19:23:10.122][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:10.124][self$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[2025-04-21 19:23:10.126][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:10.127][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 19:23:10.129][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:10.130][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 19:23:10.132][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:10.133][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 19:23:10.135][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-21 19:23:10.138][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 19:23:10.147][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:10.151][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-21 19:23:10.153][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 19:23:10.154][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:10.156][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:10.158][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:10.159][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 19:23:10.161][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:10.164][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:10.165][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 19:23:10.180][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:10.182][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:10.183][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 19:23:10.184][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:10.198][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 19:23:10.206][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 19:23:10.207][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:10.209][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:10.210][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-21 19:23:10.213][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:10.214][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-21 19:23:10.221][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:10.223][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 19:23:10.225][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:10.227][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 19:23:10.228][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:10.230][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 19:23:10.232][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-21 19:23:10.233][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 19:23:10.234][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:10.237][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-21 19:23:10.238][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 19:23:10.240][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:10.241][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:10.243][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:10.244][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 19:23:10.245][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:10.247][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:10.248][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 19:23:10.249][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:10.252][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:10.254][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 19:23:10.255][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:10.257][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 19:23:10.258][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 19:23:10.259][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:10.261][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:10.267][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 19:23:10.269][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.285][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.DEBUG[2025-04-21 19:23:10.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.360][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[2025-04-21 19:23:10.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.409][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[2025-04-21 19:23:10.411][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-21 19:23:10.412][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-21 19:23:10.415][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-21 19:23:10.417][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-21 19:23:10.421][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-21 19:23:10.424][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-21 19:23:10.426][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-21 19:23:10.427][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-21 19:23:10.429][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-21 19:23:10.430][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-21 19:23:10.432][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-21 19:23:10.434][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-21 19:23:10.436][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-21 19:23:10.438][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-21 19:23:10.440][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-21 19:23:10.442][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-21 19:23:10.444][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-21 19:23:10.445][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-21 19:23:10.447][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-21 19:23:10.448][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-21 19:23:10.449][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-21 19:23:10.451][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-21 19:23:10.452][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-21 19:23:10.453][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-21 19:23:10.454][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-21 19:23:10.458][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-21 19:23:10.460][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-21 19:23:10.461][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-21 19:23:10.464][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-21 19:23:10.466][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-21 19:23:10.468][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-21 19:23:10.470][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-21 19:23:10.472][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-21 19:23:10.474][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-21 19:23:10.477][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-21 19:23:10.478][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-21 19:23:10.480][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-21 19:23:10.481][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-21 19:23:10.483][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-21 19:23:10.485][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-21 19:23:10.488][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-21 19:23:10.490][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-21 19:23:10.492][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-21 19:23:10.494][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-21 19:23:10.496][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-21 19:23:10.498][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-21 19:23:10.503][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-21 19:23:10.506][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-21 19:23:10.507][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-21 19:23:10.509][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-21 19:23:10.511][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-21 19:23:10.513][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-21 19:23:10.515][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-21 19:23:10.516][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-21 19:23:10.521][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-21 19:23:10.522][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-21 19:23:10.524][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-21 19:23:10.525][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-21 19:23:10.527][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-21 19:23:10.529][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-21 19:23:10.531][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-21 19:23:10.533][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-21 19:23:10.535][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-21 19:23:10.537][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-21 19:23:10.541][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-21 19:23:10.544][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-21 19:23:10.546][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-21 19:23:10.548][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-21 19:23:10.549][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-21 19:23:10.551][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-21 19:23:10.554][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-21 19:23:10.555][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-21 19:23:10.556][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-21 19:23:10.558][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-21 19:23:10.559][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-21 19:23:10.560][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-21 19:23:10.561][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-21 19:23:10.562][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-21 19:23:10.564][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-21 19:23:10.567][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-21 19:23:10.569][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-21 19:23:10.570][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-21 19:23:10.572][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-21 19:23:10.573][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-21 19:23:10.576][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-21 19:23:10.577][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 19:23:10.579][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.581][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:10.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:10.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.592][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[2025-04-21 19:23:10.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:10.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:10.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.598][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[2025-04-21 19:23:10.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:10.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:10.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.606][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[2025-04-21 19:23:10.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:10.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:10.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:10.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:10.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.618][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[2025-04-21 19:23:10.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:10.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:10.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.624][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[2025-04-21 19:23:10.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:10.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:10.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:10.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:10.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:10.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:10.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:10.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:10.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.651][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[2025-04-21 19:23:10.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:10.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:10.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:10.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:10.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.663][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[2025-04-21 19:23:10.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:10.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:10.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:10.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:10.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:10.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:10.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:10.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:10.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:10.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:10.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:10.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:10.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:10.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:10.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:10.726][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-21 19:23:10.727][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-21 19:23:10.729][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:10.730][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-21 19:23:10.731][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:10.731][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 19:23:10.732][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:10.733][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 19:23:10.734][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:10.735][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-21 19:23:10.736][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-21 19:23:10.737][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 19:23:10.739][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:10.739][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-21 19:23:10.740][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 19:23:10.741][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-21 19:23:10.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-21 19:23:10.741][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-21 19:23:10.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-21 19:23:10.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-21 19:23:10.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-21 19:23:10.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-21 19:23:10.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-21 19:23:10.741][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-21 19:23:10.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-21 19:23:10.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-21 19:23:10.742][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:10.743][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 19:23:10.743][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 19:23:10.743][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 19:23:10.744][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-21 19:23:10.745][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:10.746][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:10.747][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 19:23:10.748][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:10.749][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:10.750][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 19:23:10.751][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:23:10.751][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-21 19:23:10.752][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 19:23:10.752][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 19:23:10.753][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:10.754][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-21 19:23:10.754][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-21 19:23:10.755][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-21 19:23:10.756][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-21 19:23:10.758][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-21 19:23:10.759][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-21 19:23:10.760][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-21 19:23:10.761][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-21 19:23:10.765][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-21 19:23:10.766][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-21 19:23:10.767][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-21 19:23:10.768][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-21 19:23:10.769][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-21 19:23:10.770][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-21 19:23:10.771][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-21 19:23:10.772][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-21 19:23:10.773][biodb::testThat]
biodb.INFO [2025-04-21 19:23:10.773][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2025-04-21 19:23:10.774][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:23:10.775][biodb::testThat]
biodb.DEBUG[2025-04-21 19:23:10.778][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-21 19:23:10.781][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:23:10.782][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:23:10.783][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-04-21 19:23:11.131][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-04-21 19:23:11.632][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:23:11.634][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-04-21 19:23:11.644][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-04-21 19:23:11.648][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[2025-04-21 19:23:11.650][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:23:11.651][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:23:11.653][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-21 19:23:11.985][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-21 19:23:12.355][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:23:12.357][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-04-21 19:23:12.360][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-04-21 19:23:12.362][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:12.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:12.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:12.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:12.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:12.369][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:12.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:12.371][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-21 19:23:12.374][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:23:12.374][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:23:12.377][private$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[2025-04-21 19:23:12.730][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[2025-04-21 19:23:13.105][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:23:13.107][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-04-21 19:23:13.111][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-04-21 19:23:13.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:13.114][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:13.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:13.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:13.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:13.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:13.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:13.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:13.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:13.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:13.144][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:13.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:13.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:13.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:13.151][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[2025-04-21 19:23:13.154][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 19:23:13.155][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-04-21 19:23:13.156][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 19:23:13.157][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-04-21 19:23:13.159][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:13.159][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:13.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:13.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:13.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:13.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:13.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:13.168][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[2025-04-21 19:23:13.171][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 19:23:13.172][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-04-21 19:23:13.173][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 19:23:13.175][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-04-21 19:23:13.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:13.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:13.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:13.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:13.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:13.184][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:13.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:13.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:13.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:13.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:13.192][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:13.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:13.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:13.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:13.211][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[2025-04-21 19:23:13.213][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 19:23:13.214][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-04-21 19:23:13.215][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 19:23:13.217][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-04-21 19:23:13.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:13.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:13.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:13.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:13.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:13.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:13.228][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[2025-04-21 19:23:13.229][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-21 19:23:13.232][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 19:23:13.233][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-04-21 19:23:13.234][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 19:23:13.235][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-04-21 19:23:13.237][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:13.238][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:13.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:13.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:13.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:13.245][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:13.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:13.247][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[2025-04-21 19:23:13.250][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:23:13.251][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:23:13.253][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-21 19:23:13.605][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-21 19:23:13.939][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:23:13.941][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-04-21 19:23:13.945][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-04-21 19:23:13.947][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:13.948][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:13.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:13.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:13.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:13.956][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:13.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-21 19:23:13.965][biodb::testThat]
biodb.INFO [2025-04-21 19:23:13.966][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2025-04-21 19:23:13.967][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:23:13.968][biodb::testThat]
biodb.DEBUG[2025-04-21 19:23:13.970][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-21 19:23:13.974][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:23:13.975][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:23:13.976][private$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[2025-04-21 19:23:14.383][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[2025-04-21 19:23:16.482][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:23:16.484][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-04-21 19:23:16.499][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-04-21 19:23:16.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:16.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:16.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:16.509][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:16.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:16.522][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:16.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:16.527][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[2025-04-21 19:23:16.529][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:23:16.530][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:23:16.532][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-21 19:23:16.911][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-21 19:23:17.243][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:23:17.244][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-04-21 19:23:17.249][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-04-21 19:23:17.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:17.252][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:17.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:17.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-21 19:23:17.303][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-21 19:23:17.304][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-21 19:23:17.305][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-21 19:23:17.306][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-21 19:23:17.306][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:17.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:17.308][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.309][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-21 19:23:17.314][biodb::testContext]
biodb.INFO [2025-04-21 19:23:17.315][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-21 19:23:17.316][biodb::testContext] Test context - Test web services
biodb.INFO [2025-04-21 19:23:17.317][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-21 19:23:17.317][biodb::testContext]
biodb.INFO [2025-04-21 19:23:17.319][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-21 19:23:17.322][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-21 19:23:17.328][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 19:23:17.329][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-21 19:23:17.329][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-21 19:23:17.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.332][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-21 19:23:17.333][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-21 19:23:17.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.336][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-21 19:23:17.336][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-21 19:23:17.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.339][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[2025-04-21 19:23:17.340][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-21 19:23:17.341][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-21 19:23:17.342][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-21 19:23:17.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.345][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-21 19:23:17.346][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-21 19:23:17.346][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-21 19:23:17.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.350][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-21 19:23:17.351][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-21 19:23:17.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.354][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-21 19:23:17.355][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-21 19:23:17.355][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-21 19:23:17.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.358][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-21 19:23:17.359][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-21 19:23:17.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.362][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-21 19:23:17.363][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-21 19:23:17.364][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-21 19:23:17.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.367][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-21 19:23:17.367][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-21 19:23:17.368][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-21 19:23:17.369][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-21 19:23:17.370][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-21 19:23:17.370][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-21 19:23:17.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.374][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-21 19:23:17.375][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-21 19:23:17.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.377][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[2025-04-21 19:23:17.378][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-21 19:23:17.379][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-21 19:23:17.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.382][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-21 19:23:17.383][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-21 19:23:17.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.398][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-21 19:23:17.399][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-21 19:23:17.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.402][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-21 19:23:17.403][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-21 19:23:17.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.406][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-21 19:23:17.407][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-21 19:23:17.532][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-21 19:23:17.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.536][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-21 19:23:17.538][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-21 19:23:17.539][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-21 19:23:17.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.552][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[2025-04-21 19:23:17.553][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-21 19:23:17.555][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:17.556][self$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[2025-04-21 19:23:17.557][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:17.558][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 19:23:17.559][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:17.560][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 19:23:17.561][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:17.562][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 19:23:17.563][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-21 19:23:17.564][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 19:23:17.564][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:17.565][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-21 19:23:17.566][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 19:23:17.567][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:17.568][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:17.569][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 19:23:17.569][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 19:23:17.569][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 19:23:17.569][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-21 19:23:17.569][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-21 19:23:17.583][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 19:23:17.584][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:17.585][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:17.586][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 19:23:17.587][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:17.587][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:17.588][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 19:23:17.589][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:17.590][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 19:23:17.590][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 19:23:17.591][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:17.592][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:17.593][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-21 19:23:17.595][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:17.595][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-21 19:23:17.596][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:17.597][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 19:23:17.598][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:17.599][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 19:23:17.600][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:17.601][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 19:23:17.602][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-21 19:23:17.603][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 19:23:17.603][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:17.604][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-21 19:23:17.605][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 19:23:17.606][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:17.607][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:17.608][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 19:23:17.608][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 19:23:17.608][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 19:23:17.608][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-21 19:23:17.608][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-21 19:23:17.609][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 19:23:17.610][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:17.610][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:17.611][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 19:23:17.612][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:17.613][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:17.614][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 19:23:17.614][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:17.615][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 19:23:17.616][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 19:23:17.617][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:17.618][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:17.619][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-21 19:23:17.620][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:17.621][self$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[2025-04-21 19:23:17.622][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:17.623][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 19:23:17.624][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:17.625][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 19:23:17.626][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:17.627][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 19:23:17.628][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-21 19:23:17.628][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 19:23:17.629][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:17.630][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-21 19:23:17.631][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 19:23:17.632][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:17.633][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:17.634][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:17.634][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 19:23:17.635][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:17.636][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:17.637][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 19:23:17.637][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:17.638][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:17.639][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 19:23:17.640][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:17.641][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 19:23:17.641][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 19:23:17.642][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:17.643][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:17.644][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-21 19:23:17.645][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:17.646][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-21 19:23:17.647][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:17.648][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 19:23:17.649][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:17.650][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 19:23:17.651][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:17.652][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 19:23:17.653][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-21 19:23:17.653][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 19:23:17.654][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:17.656][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-21 19:23:17.667][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 19:23:17.668][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:17.669][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:17.670][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:17.671][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 19:23:17.672][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:17.672][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:17.673][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 19:23:17.674][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:17.675][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:17.676][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 19:23:17.677][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:17.678][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 19:23:17.679][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 19:23:17.680][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:17.682][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:17.696][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 19:23:17.697][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.705][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.DEBUG[2025-04-21 19:23:17.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.731][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[2025-04-21 19:23:17.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.735][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[2025-04-21 19:23:17.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.739][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[2025-04-21 19:23:17.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.742][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[2025-04-21 19:23:17.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.749][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[2025-04-21 19:23:17.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.767][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[2025-04-21 19:23:17.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.792][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-21 19:23:17.793][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-21 19:23:17.795][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-21 19:23:17.796][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-21 19:23:17.797][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-21 19:23:17.799][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-21 19:23:17.800][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-21 19:23:17.801][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-21 19:23:17.802][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-21 19:23:17.804][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-21 19:23:17.828][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-21 19:23:17.830][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-21 19:23:17.837][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-21 19:23:17.839][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-21 19:23:17.844][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-21 19:23:17.847][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-21 19:23:17.849][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-21 19:23:17.851][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-21 19:23:17.855][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-21 19:23:17.857][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-21 19:23:17.858][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-21 19:23:17.859][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-21 19:23:17.860][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-21 19:23:17.861][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-21 19:23:17.862][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-21 19:23:17.863][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-21 19:23:17.865][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-21 19:23:17.866][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-21 19:23:17.867][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-21 19:23:17.869][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-21 19:23:17.871][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-21 19:23:17.872][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-21 19:23:17.873][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-21 19:23:17.874][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-21 19:23:17.875][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-21 19:23:17.876][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-21 19:23:17.877][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-21 19:23:17.878][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-21 19:23:17.880][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-21 19:23:17.882][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-21 19:23:17.884][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-21 19:23:17.885][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-21 19:23:17.886][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-21 19:23:17.888][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-21 19:23:17.889][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-21 19:23:17.890][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-21 19:23:17.891][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-21 19:23:17.893][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-21 19:23:17.894][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-21 19:23:17.896][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-21 19:23:17.897][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-21 19:23:17.898][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-21 19:23:17.899][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-21 19:23:17.900][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-21 19:23:17.901][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-21 19:23:17.902][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-21 19:23:17.904][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-21 19:23:17.906][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-21 19:23:17.907][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-21 19:23:17.908][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-21 19:23:17.909][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-21 19:23:17.911][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-21 19:23:17.912][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-21 19:23:17.913][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-21 19:23:17.914][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-21 19:23:17.916][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-21 19:23:17.918][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-21 19:23:17.920][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-21 19:23:17.922][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-21 19:23:17.923][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-21 19:23:17.925][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-21 19:23:17.927][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-21 19:23:17.929][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-21 19:23:17.931][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-21 19:23:17.932][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-21 19:23:17.935][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-21 19:23:17.936][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-21 19:23:17.938][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-21 19:23:17.940][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-21 19:23:17.941][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-21 19:23:17.942][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-21 19:23:17.944][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-21 19:23:17.945][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-21 19:23:17.946][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-21 19:23:17.949][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-21 19:23:17.950][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 19:23:17.951][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.953][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:17.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:17.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:17.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:17.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:17.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:17.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.974][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[2025-04-21 19:23:17.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:17.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:17.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.981][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[2025-04-21 19:23:17.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:17.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:17.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:17.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:17.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:17.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:17.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:17.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:17.996][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[2025-04-21 19:23:17.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:17.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:17.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:18.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:18.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:18.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:18.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:18.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:18.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:18.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:18.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:18.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:18.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:18.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:18.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:18.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:18.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:18.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:18.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:18.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:18.015][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[2025-04-21 19:23:18.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:18.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:18.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:18.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:18.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:18.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:18.021][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[2025-04-21 19:23:18.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:18.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:18.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:18.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:18.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:18.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:18.029][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[2025-04-21 19:23:18.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:18.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:18.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:18.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:18.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:18.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:18.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:18.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:18.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:18.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:18.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:18.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:18.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:18.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:18.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:18.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:18.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:18.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:18.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:18.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:18.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:18.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:18.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:18.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:18.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:18.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:18.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:18.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:18.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:18.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:18.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:18.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:18.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:18.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:18.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:18.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:18.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:18.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:18.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:18.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:18.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:18.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:18.072][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-21 19:23:18.074][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-21 19:23:18.076][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:18.077][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-21 19:23:18.078][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:18.079][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 19:23:18.080][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:18.081][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 19:23:18.082][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:18.083][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-21 19:23:18.085][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-21 19:23:18.086][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 19:23:18.087][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:18.088][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-21 19:23:18.089][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 19:23:18.090][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-21 19:23:18.090][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-21 19:23:18.090][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-21 19:23:18.090][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-21 19:23:18.090][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-21 19:23:18.090][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-21 19:23:18.090][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-21 19:23:18.090][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-21 19:23:18.090][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-21 19:23:18.090][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-21 19:23:18.090][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-21 19:23:18.091][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:18.092][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 19:23:18.092][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 19:23:18.092][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 19:23:18.093][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-21 19:23:18.093][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:18.094][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:18.095][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 19:23:18.096][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:18.099][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:18.100][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 19:23:18.101][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:23:18.101][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-21 19:23:18.102][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 19:23:18.103][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 19:23:18.104][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:18.105][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-21 19:23:18.105][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-21 19:23:18.106][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-21 19:23:18.107][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-21 19:23:18.109][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-21 19:23:18.111][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-21 19:23:18.112][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-21 19:23:18.114][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-21 19:23:18.117][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-21 19:23:18.118][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-21 19:23:18.119][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-21 19:23:18.120][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-21 19:23:18.122][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-21 19:23:18.124][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-21 19:23:18.125][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-21 19:23:18.126][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-21 19:23:18.127][biodb::testThat]
biodb.INFO [2025-04-21 19:23:18.128][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-04-21 19:23:18.129][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:23:18.130][biodb::testThat]
biodb.DEBUG[2025-04-21 19:23:18.134][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-21 19:23:18.138][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 19:23:18.140][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-04-21 19:23:18.142][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 19:23:18.144][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-04-21 19:23:18.161][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-21 19:23:18.167][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:23:18.168][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:23:18.169][private$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[2025-04-21 19:23:18.514][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[2025-04-21 19:23:18.849][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:23:18.853][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-04-21 19:23:18.859][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-04-21 19:23:18.880][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-21 19:23:18.882][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-21 19:23:18.884][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-21 19:23:18.885][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-21 19:23:18.887][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:18.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:18.889][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:18.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:18.891][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:18.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-21 19:23:18.899][biodb::testContext]
biodb.INFO [2025-04-21 19:23:18.903][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-21 19:23:18.907][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-04-21 19:23:18.908][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-21 19:23:18.910][biodb::testContext]
biodb.INFO [2025-04-21 19:23:18.914][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-21 19:23:18.917][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-21 19:23:18.925][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 19:23:18.927][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-21 19:23:18.928][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-21 19:23:18.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:18.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:18.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:18.936][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-21 19:23:18.942][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-21 19:23:18.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:18.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:18.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:18.952][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-21 19:23:18.974][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-21 19:23:18.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:18.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:18.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:18.980][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-21 19:23:18.982][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-21 19:23:18.998][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-21 19:23:19.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.006][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-21 19:23:19.007][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-21 19:23:19.010][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-21 19:23:19.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.015][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-21 19:23:19.017][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-21 19:23:19.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.025][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-21 19:23:19.026][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-21 19:23:19.028][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-21 19:23:19.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.035][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-21 19:23:19.037][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-21 19:23:19.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.042][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-21 19:23:19.044][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-21 19:23:19.048][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-21 19:23:19.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.053][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-21 19:23:19.054][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-21 19:23:19.056][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-21 19:23:19.058][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-21 19:23:19.062][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-21 19:23:19.063][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-21 19:23:19.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.067][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[2025-04-21 19:23:19.069][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-21 19:23:19.071][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-21 19:23:19.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.077][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-21 19:23:19.079][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-21 19:23:19.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.084][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-21 19:23:19.085][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-21 19:23:19.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.090][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-21 19:23:19.092][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-21 19:23:19.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.095][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[2025-04-21 19:23:19.097][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-21 19:23:19.098][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-21 19:23:19.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.105][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-21 19:23:19.107][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-21 19:23:19.212][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-21 19:23:19.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.216][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[2025-04-21 19:23:19.218][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-21 19:23:19.219][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-21 19:23:19.221][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-21 19:23:19.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.227][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-21 19:23:19.230][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:19.231][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-21 19:23:19.233][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:19.236][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 19:23:19.238][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:19.240][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 19:23:19.241][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:19.242][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 19:23:19.244][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-21 19:23:19.245][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 19:23:19.248][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:19.250][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-21 19:23:19.251][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 19:23:19.252][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:19.254][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:19.255][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 19:23:19.255][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 19:23:19.255][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 19:23:19.255][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-21 19:23:19.255][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-21 19:23:19.256][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 19:23:19.258][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:19.258][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:19.259][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 19:23:19.260][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:19.261][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:19.262][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 19:23:19.263][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:19.264][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 19:23:19.266][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 19:23:19.267][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:19.272][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:19.274][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-21 19:23:19.277][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:19.279][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-21 19:23:19.280][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:19.282][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 19:23:19.283][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:19.285][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 19:23:19.286][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:19.287][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 19:23:19.290][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-21 19:23:19.291][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 19:23:19.292][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:19.293][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-21 19:23:19.294][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 19:23:19.295][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:19.296][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:19.297][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 19:23:19.297][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 19:23:19.297][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 19:23:19.297][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-21 19:23:19.297][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-21 19:23:19.298][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 19:23:19.299][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:19.300][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:19.300][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 19:23:19.318][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:19.319][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:19.320][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 19:23:19.322][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:19.323][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 19:23:19.325][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 19:23:19.326][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:19.332][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:19.334][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-21 19:23:19.336][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:19.338][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-21 19:23:19.341][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:19.343][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 19:23:19.344][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:19.346][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 19:23:19.347][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:19.349][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 19:23:19.350][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-21 19:23:19.351][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 19:23:19.355][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:19.356][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-21 19:23:19.358][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 19:23:19.359][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:19.361][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:19.363][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:19.364][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 19:23:19.366][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:19.369][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:19.370][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 19:23:19.371][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:19.373][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:19.375][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 19:23:19.376][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:19.378][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 19:23:19.379][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 19:23:19.381][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:19.383][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:19.384][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-21 19:23:19.387][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:19.388][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-21 19:23:19.390][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:19.394][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 19:23:19.396][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:19.397][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 19:23:19.399][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:19.400][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-21 19:23:19.402][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-21 19:23:19.405][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 19:23:19.407][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:19.408][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-21 19:23:19.410][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 19:23:19.411][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:19.412][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:19.413][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:19.415][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-21 19:23:19.416][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:19.417][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:19.418][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 19:23:19.419][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:19.420][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:19.421][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 19:23:19.422][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:19.423][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 19:23:19.427][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 19:23:19.431][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:19.433][self$setPropertyValue]
biodb.DEBUG[2025-04-21 19:23:19.436][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 19:23:19.437][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.473][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.DEBUG[2025-04-21 19:23:19.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.491][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[2025-04-21 19:23:19.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.543][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[2025-04-21 19:23:19.545][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-21 19:23:19.554][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-21 19:23:19.556][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-21 19:23:19.559][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-21 19:23:19.561][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-21 19:23:19.566][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-21 19:23:19.568][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-21 19:23:19.571][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-21 19:23:19.573][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-21 19:23:19.575][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-21 19:23:19.580][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-21 19:23:19.582][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-21 19:23:19.584][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-21 19:23:19.586][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-21 19:23:19.593][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-21 19:23:19.595][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-21 19:23:19.602][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-21 19:23:19.604][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-21 19:23:19.612][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-21 19:23:19.614][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-21 19:23:19.616][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-21 19:23:19.618][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-21 19:23:19.623][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-21 19:23:19.625][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-21 19:23:19.627][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-21 19:23:19.629][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-21 19:23:19.631][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-21 19:23:19.654][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-21 19:23:19.657][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-21 19:23:19.659][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-21 19:23:19.661][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-21 19:23:19.674][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-21 19:23:19.676][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-21 19:23:19.679][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-21 19:23:19.681][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-21 19:23:19.693][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-21 19:23:19.696][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-21 19:23:19.698][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-21 19:23:19.718][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-21 19:23:19.721][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-21 19:23:19.726][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-21 19:23:19.728][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-21 19:23:19.731][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-21 19:23:19.733][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-21 19:23:19.735][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-21 19:23:19.737][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-21 19:23:19.743][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-21 19:23:19.746][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-21 19:23:19.748][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-21 19:23:19.750][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-21 19:23:19.752][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-21 19:23:19.754][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-21 19:23:19.756][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-21 19:23:19.758][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-21 19:23:19.760][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-21 19:23:19.762][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-21 19:23:19.765][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-21 19:23:19.768][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-21 19:23:19.770][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-21 19:23:19.772][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-21 19:23:19.774][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-21 19:23:19.776][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-21 19:23:19.803][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-21 19:23:19.805][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-21 19:23:19.808][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-21 19:23:19.810][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-21 19:23:19.812][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-21 19:23:19.814][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-21 19:23:19.816][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-21 19:23:19.818][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-21 19:23:19.820][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-21 19:23:19.823][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-21 19:23:19.825][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-21 19:23:19.827][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-21 19:23:19.829][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-21 19:23:19.831][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-21 19:23:19.838][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-21 19:23:19.840][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-21 19:23:19.842][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-21 19:23:19.844][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-21 19:23:19.846][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-21 19:23:19.849][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-21 19:23:19.860][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-21 19:23:19.865][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-21 19:23:19.877][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-21 19:23:19.878][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-21 19:23:19.879][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.883][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:19.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:19.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:19.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:19.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:19.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:19.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:19.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:19.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:19.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:19.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.969][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.DEBUG[2025-04-21 19:23:19.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:19.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:19.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:19.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:19.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:19.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:19.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:19.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:19.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:19.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:19.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:19.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:20.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:20.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:20.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:20.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:20.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:20.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:20.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:20.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:20.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:20.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:20.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:20.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:20.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:20.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:20.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:20.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:20.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:20.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:20.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:20.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:20.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:20.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:20.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:20.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:20.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:20.031][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.DEBUG[2025-04-21 19:23:20.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:20.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:20.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:20.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:20.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:20.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:20.042][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[2025-04-21 19:23:20.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:20.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:20.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:20.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:20.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:20.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:20.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:20.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:20.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:20.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:20.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:20.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:20.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:20.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:20.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:20.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:20.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:20.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:20.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:20.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:20.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:20.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-21 19:23:20.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:20.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:20.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:20.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:20.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:20.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:20.091][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-21 19:23:20.093][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-21 19:23:20.095][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:20.096][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-21 19:23:20.097][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:20.097][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-21 19:23:20.098][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:20.099][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-21 19:23:20.100][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:20.102][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-21 19:23:20.107][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-21 19:23:20.109][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-21 19:23:20.111][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:20.113][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-21 19:23:20.114][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-21 19:23:20.117][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-21 19:23:20.117][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-21 19:23:20.117][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-21 19:23:20.117][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-21 19:23:20.117][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-21 19:23:20.117][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-21 19:23:20.117][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-21 19:23:20.117][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-21 19:23:20.117][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-21 19:23:20.117][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-21 19:23:20.117][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-21 19:23:20.119][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-21 19:23:20.120][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-21 19:23:20.120][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-21 19:23:20.120][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-21 19:23:20.122][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-21 19:23:20.124][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:20.125][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:20.126][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-21 19:23:20.128][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-21 19:23:20.129][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-21 19:23:20.130][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-21 19:23:20.131][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:23:20.131][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-21 19:23:20.133][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-21 19:23:20.135][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-21 19:23:20.136][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-21 19:23:20.138][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-21 19:23:20.138][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-21 19:23:20.140][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-21 19:23:20.143][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-21 19:23:20.145][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-21 19:23:20.147][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-21 19:23:20.150][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-21 19:23:20.153][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-21 19:23:20.159][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-21 19:23:20.160][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-21 19:23:20.163][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-21 19:23:20.165][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-21 19:23:20.167][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-21 19:23:20.168][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-21 19:23:20.170][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-21 19:23:20.171][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-21 19:23:20.173][biodb::testThat]
biodb.INFO [2025-04-21 19:23:20.174][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-04-21 19:23:20.176][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-21 19:23:20.177][biodb::testThat]
biodb.DEBUG[2025-04-21 19:23:20.183][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-21 19:23:20.188][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 19:23:20.194][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-04-21 19:23:20.196][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 19:23:20.199][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-04-21 19:23:20.205][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[2025-04-21 19:23:20.210][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-21 19:23:20.212][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-04-21 19:23:20.215][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-21 19:23:20.217][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-04-21 19:23:20.221][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-04-21 19:23:20.222][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-21 19:23:20.224][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-04-21 19:23:20.226][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-21 19:23:20.227][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-21 19:23:20.234][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-21 19:23:20.236][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-21 19:23:20.238][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-21 19:23:20.239][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-21 19:23:20.246][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:20.248][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:20.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:20.262][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:20.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:20.265][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:20.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-21 19:23:20.270][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-04-21 19:23:20.274][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-21 19:23:20.276][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-21 19:23:20.278][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-04-21 19:23:20.630][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-04-21 19:23:21.696][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-21 19:23:21.699][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-04-21 19:23:21.706][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-04-21 19:23:21.710][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-04-21 19:23:21.714][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-21 19:23:21.716][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-21 19:23:21.717][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-21 19:23:21.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-21 19:23:21.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:21.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:21.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:21.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:21.734][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:21.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-21 19:23:21.742][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:21.744][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:21.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:21.747][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:21.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:21.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:21.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:21.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:21.757][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:23:21.758][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:23:21.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:21.762][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:21.764][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-21 19:23:21.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-21 19:23:21.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:21.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:21.769][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:23:21.776][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:23:21.778][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:21.779][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:21.781][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-21 19:23:21.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-21 19:23:21.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:21.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:21.795][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-21 19:23:21.798][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-21 19:23:21.838][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:21.840][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:21.843][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-21 19:23:21.852][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-21 19:23:21.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:21.855][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:21.858][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:23:21.860][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:23:21.868][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:21.870][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:21.874][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:23:21.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-21 19:23:21.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:21.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:21.887][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:23:21.889][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:21.891][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:21.892][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:21.902][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-21 19:23:21.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-21 19:23:21.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:21.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:21.909][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:21.911][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:21.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:21.919][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:21.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:21.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-21 19:23:21.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:21.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:21.936][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:23:21.938][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:23:21.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:21.940][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:21.943][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-21 19:23:21.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-21 19:23:21.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:21.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:21.959][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:23:21.961][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:23:21.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:21.969][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:21.972][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-21 19:23:21.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-21 19:23:21.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:21.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:21.987][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:23:21.990][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:23:21.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:21.993][ef$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:22.003][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-21 19:23:22.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-21 19:23:22.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:22.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:22.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:22.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:22.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:22.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:22.026][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:22.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:22.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:22.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:22.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:22.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:22.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:22.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:22.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-21 19:23:22.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-21 19:23:22.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:22.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:22.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:22.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:22.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:22.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:22.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:22.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:22.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:22.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:22.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:22.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:22.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:22.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:22.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:22.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:22.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:22.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:22.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:22.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:22.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:22.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-21 19:23:22.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-21 19:23:22.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-21 19:23:22.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-21 19:23:22.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-21 19:23:22.131][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-04-21 19:23:22.155][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-21 19:23:22.158][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-21 19:23:22.160][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-21 19:23:22.161][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-21 19:23:22.163][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-21 19:23:22.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-21 19:23:22.170][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-21 19:23:22.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-21 19:23:22.173][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-21 19:23:22.174][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
>
> proc.time()
user system elapsed
24.794 1.685 71.970
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 2.648 | 1.079 | 7.972 | |
| ChebiEntry | 0.355 | 0.015 | 0.390 | |