Pierrick Roger
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_20 |
| git_last_commit: e6b963e |
| git_last_commit_date: 2024-10-29 11:04:35 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 202/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.12.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2024-12-20 00:18:06 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 00:21:26 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 199.8 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* 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 ‘1.12.0’
* 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 4.747 1.247 7.006
* 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/4.4-x86_64/Resources/library’ * installing *source* package ‘biodbChebi’ ... ** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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 [2024-12-20 00:19:39.678][biodb::testContext]
biodb.INFO [2024-12-20 00:19:39.686][biodb::testContext] ********************************************************************************
biodb.INFO [2024-12-20 00:19:39.689][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-12-20 00:19:39.692][biodb::testContext] ********************************************************************************
biodb.INFO [2024-12-20 00:19:39.694][biodb::testContext]
biodb.INFO [2024-12-20 00:19:39.707][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-12-20 00:19:39.712][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-12-20 00:19:39.729][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 00:19:39.732][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-12-20 00:19:39.735][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-12-20 00:19:39.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:39.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:39.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:39.746][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-12-20 00:19:39.806][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-12-20 00:19:39.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:39.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:39.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:39.818][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-12-20 00:19:39.821][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-12-20 00:19:39.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:39.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:39.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:39.832][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-12-20 00:19:39.835][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-12-20 00:19:39.838][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-12-20 00:19:39.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:39.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:39.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:39.868][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-12-20 00:19:39.871][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-12-20 00:19:39.874][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-12-20 00:19:39.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:39.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:39.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:39.883][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-12-20 00:19:39.886][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-12-20 00:19:39.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:39.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:39.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:39.895][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-12-20 00:19:39.897][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-12-20 00:19:39.900][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-12-20 00:19:39.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:39.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:39.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:39.909][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-12-20 00:19:39.912][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-12-20 00:19:39.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:39.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:39.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:39.921][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-12-20 00:19:39.924][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-12-20 00:19:39.927][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-12-20 00:19:39.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:39.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:39.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:39.937][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-12-20 00:19:39.940][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-12-20 00:19:39.943][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-12-20 00:19:39.946][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-12-20 00:19:39.949][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-12-20 00:19:39.951][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-12-20 00:19:39.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:39.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:39.958][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[2024-12-20 00:19:39.961][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-12-20 00:19:39.963][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-12-20 00:19:39.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:39.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:39.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:39.973][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-12-20 00:19:39.976][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-12-20 00:19:39.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:39.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:39.983][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.DEBUG[2024-12-20 00:19:39.985][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-12-20 00:19:39.988][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-12-20 00:19:39.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:39.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:39.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:39.997][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-12-20 00:19:40.000][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-12-20 00:19:40.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:40.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.007][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[2024-12-20 00:19:40.009][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-12-20 00:19:40.012][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-12-20 00:19:40.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:40.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:40.021][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-12-20 00:19:40.024][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-12-20 00:19:40.045][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-12-20 00:19:40.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:40.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.051][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[2024-12-20 00:19:40.053][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-12-20 00:19:40.055][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-12-20 00:19:40.058][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-12-20 00:19:40.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:40.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:40.071][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-12-20 00:19:40.158][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 00:19:40.231][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-12-20 00:19:40.233][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 00:19:40.235][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 00:19:40.238][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 00:19:40.240][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 00:19:40.243][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 00:19:40.245][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 00:19:40.247][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-12-20 00:19:40.250][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 00:19:40.252][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 00:19:40.254][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-12-20 00:19:40.257][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 00:19:40.259][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:19:40.261][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 00:19:40.263][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 00:19:40.263][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 00:19:40.263][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 00:19:40.263][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-12-20 00:19:40.263][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-12-20 00:19:40.266][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 00:19:40.270][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:19:40.272][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:19:40.275][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 00:19:40.277][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:19:40.279][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:19:40.282][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 00:19:40.284][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:19:40.286][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 00:19:40.288][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 00:19:40.291][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 00:19:40.293][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:19:40.296][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-12-20 00:19:40.301][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 00:19:40.303][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-12-20 00:19:40.306][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 00:19:40.308][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 00:19:40.311][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 00:19:40.313][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 00:19:40.315][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 00:19:40.318][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 00:19:40.320][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-12-20 00:19:40.323][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 00:19:40.325][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 00:19:40.328][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-12-20 00:19:40.330][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 00:19:40.333][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:19:40.335][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 00:19:40.367][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 00:19:40.367][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 00:19:40.367][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 00:19:40.367][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-12-20 00:19:40.367][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-12-20 00:19:40.370][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 00:19:40.372][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:19:40.374][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:19:40.376][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 00:19:40.379][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:19:40.381][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:19:40.384][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 00:19:40.386][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:19:40.388][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 00:19:40.390][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 00:19:40.392][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 00:19:40.395][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:19:40.398][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-12-20 00:19:40.402][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-12-20 00:19:40.404][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-12-20 00:19:40.407][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 00:19:40.410][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 00:19:40.413][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 00:19:40.416][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 00:19:40.418][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 00:19:40.429][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 00:19:40.432][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-12-20 00:19:40.434][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 00:19:40.436][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-12-20 00:19:40.439][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-12-20 00:19:40.442][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 00:19:40.444][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:19:40.446][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 00:19:40.449][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:19:40.451][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 00:19:40.455][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:19:40.458][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:19:40.460][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 00:19:40.462][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:19:40.464][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:19:40.468][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 00:19:40.470][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:19:40.473][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 00:19:40.475][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 00:19:40.477][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 00:19:40.480][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:19:40.483][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-12-20 00:19:40.488][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-12-20 00:19:40.490][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-12-20 00:19:40.492][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 00:19:40.495][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 00:19:40.497][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 00:19:40.499][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 00:19:40.502][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 00:19:40.504][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 00:19:40.506][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-12-20 00:19:40.509][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 00:19:40.537][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-12-20 00:19:40.539][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-12-20 00:19:40.543][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 00:19:40.545][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:19:40.547][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 00:19:40.550][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:19:40.552][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 00:19:40.555][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:19:40.557][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:19:40.559][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 00:19:40.562][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:19:40.564][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:19:40.567][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 00:19:40.570][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:19:40.573][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 00:19:40.575][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 00:19:40.577][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 00:19:40.580][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:19:40.587][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 00:19:40.589][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.591][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.DEBUG[2024-12-20 00:19:40.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:40.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:40.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:40.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:40.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:40.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:40.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:40.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.612][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[2024-12-20 00:19:40.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:40.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:40.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:40.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:40.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:40.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:40.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:40.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:40.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:40.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:40.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:40.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.644][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[2024-12-20 00:19:40.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:40.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:40.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:40.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:40.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:40.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:40.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:40.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:40.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:40.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:40.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:40.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.676][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[2024-12-20 00:19:40.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:40.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:40.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:40.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:40.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:40.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:40.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:40.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.728][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[2024-12-20 00:19:40.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:40.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:40.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:40.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:40.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:40.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:40.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:40.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.751][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[2024-12-20 00:19:40.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:40.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:40.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:40.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:40.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:40.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:40.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:40.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.771][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[2024-12-20 00:19:40.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:40.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:40.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:40.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:40.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:40.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:40.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:40.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:40.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:40.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:40.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:40.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:40.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:40.804][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-12-20 00:19:40.813][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-12-20 00:19:40.817][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-12-20 00:19:40.820][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-12-20 00:19:40.824][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-12-20 00:19:40.827][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-12-20 00:19:40.831][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-12-20 00:19:40.834][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-12-20 00:19:40.838][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-12-20 00:19:40.841][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-12-20 00:19:40.844][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-12-20 00:19:40.848][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-12-20 00:19:40.852][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-12-20 00:19:40.855][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-12-20 00:19:40.859][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-12-20 00:19:40.862][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-12-20 00:19:40.896][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-12-20 00:19:40.900][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-12-20 00:19:40.903][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-12-20 00:19:40.907][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-12-20 00:19:40.910][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-12-20 00:19:40.913][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-12-20 00:19:40.917][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-12-20 00:19:40.920][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-12-20 00:19:40.923][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-12-20 00:19:40.927][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-12-20 00:19:40.930][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-12-20 00:19:40.933][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-12-20 00:19:40.936][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-12-20 00:19:40.939][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-12-20 00:19:40.943][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-12-20 00:19:40.946][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-12-20 00:19:40.949][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-12-20 00:19:40.952][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-12-20 00:19:40.956][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-12-20 00:19:40.959][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-12-20 00:19:40.962][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-12-20 00:19:40.965][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-12-20 00:19:40.969][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-12-20 00:19:40.972][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-12-20 00:19:40.975][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-12-20 00:19:40.979][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-12-20 00:19:40.991][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-12-20 00:19:40.994][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-12-20 00:19:40.998][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-12-20 00:19:41.001][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-12-20 00:19:41.004][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-12-20 00:19:41.008][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-12-20 00:19:41.012][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-12-20 00:19:41.015][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-12-20 00:19:41.018][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-12-20 00:19:41.022][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-12-20 00:19:41.025][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-12-20 00:19:41.029][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-12-20 00:19:41.032][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-12-20 00:19:41.035][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-12-20 00:19:41.038][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-12-20 00:19:41.042][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-12-20 00:19:41.078][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-12-20 00:19:41.082][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-12-20 00:19:41.086][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-12-20 00:19:41.089][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-12-20 00:19:41.093][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-12-20 00:19:41.097][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-12-20 00:19:41.101][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-12-20 00:19:41.104][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-12-20 00:19:41.108][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-12-20 00:19:41.111][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-12-20 00:19:41.115][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-12-20 00:19:41.118][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-12-20 00:19:41.121][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-12-20 00:19:41.124][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-12-20 00:19:41.127][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-12-20 00:19:41.130][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-12-20 00:19:41.134][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-12-20 00:19:41.137][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-12-20 00:19:41.141][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-12-20 00:19:41.145][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-12-20 00:19:41.148][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-12-20 00:19:41.152][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-12-20 00:19:41.155][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-12-20 00:19:41.158][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-12-20 00:19:41.161][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-12-20 00:19:41.176][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-12-20 00:19:41.180][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-12-20 00:19:41.186][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 00:19:41.188][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:41.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:41.192][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:41.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:41.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:41.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:41.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:41.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:41.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:41.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:41.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:41.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:41.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:41.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:41.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:41.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:41.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:41.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:41.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:41.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:41.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:41.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:41.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:41.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:41.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:41.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:41.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:41.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:41.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:41.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:41.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:41.290][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[2024-12-20 00:19:41.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:41.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:41.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:41.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:41.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:41.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:41.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:41.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:41.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:41.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:41.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:41.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:41.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:41.319][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[2024-12-20 00:19:41.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:41.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:41.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:41.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:41.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:41.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:41.333][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[2024-12-20 00:19:41.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:41.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:41.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:41.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:41.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:41.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:41.353][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[2024-12-20 00:19:41.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:41.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:41.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:41.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:41.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:41.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:41.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:41.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:41.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:41.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:41.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:41.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:41.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:41.381][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[2024-12-20 00:19:41.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:41.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:41.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:41.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:41.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:41.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:41.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:41.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:41.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:41.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:41.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:41.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:41.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:41.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:41.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:41.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:41.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:41.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:41.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:41.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:41.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:41.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:41.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:41.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:41.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:41.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:41.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:41.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:41.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:41.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:41.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:41.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:41.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:41.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:41.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:41.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:41.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:41.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:41.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:41.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:41.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:41.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:41.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:19:41.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:41.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:41.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:41.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:41.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:41.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:41.515][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-12-20 00:19:41.547][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-12-20 00:19:41.552][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 00:19:41.555][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-12-20 00:19:41.557][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 00:19:41.560][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 00:19:41.562][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 00:19:41.565][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 00:19:41.567][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-12-20 00:19:41.597][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-12-20 00:19:41.600][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-12-20 00:19:41.603][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 00:19:41.605][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 00:19:41.608][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-12-20 00:19:41.611][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 00:19:41.613][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-12-20 00:19:41.613][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-12-20 00:19:41.613][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-12-20 00:19:41.613][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-12-20 00:19:41.613][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-12-20 00:19:41.613][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-12-20 00:19:41.613][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-12-20 00:19:41.613][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-12-20 00:19:41.613][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-12-20 00:19:41.613][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-12-20 00:19:41.613][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-12-20 00:19:41.616][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-12-20 00:19:41.619][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 00:19:41.619][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 00:19:41.619][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 00:19:41.622][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-12-20 00:19:41.624][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:19:41.626][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:19:41.629][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 00:19:41.631][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:19:41.633][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:19:41.635][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 00:19:41.638][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:19:41.638][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-12-20 00:19:41.640][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 00:19:41.642][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 00:19:41.645][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-12-20 00:19:41.647][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-12-20 00:19:41.647][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-12-20 00:19:41.663][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-12-20 00:19:41.666][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-12-20 00:19:41.670][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-12-20 00:19:41.674][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-12-20 00:19:41.679][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-12-20 00:19:41.683][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-12-20 00:19:41.730][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-12-20 00:19:41.733][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-12-20 00:19:41.741][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-12-20 00:19:41.749][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-12-20 00:19:41.757][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-12-20 00:19:41.759][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-12-20 00:19:41.762][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-12-20 00:19:41.765][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-12-20 00:19:41.784][biodb::testThat]
biodb.INFO [2024-12-20 00:19:41.786][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-12-20 00:19:41.788][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:19:41.791][biodb::testThat]
biodb.TRACE[2024-12-20 00:19:41.799][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-12-20 00:19:41.803][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:19:41.810][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:19:41.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:19:41.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:41.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:41.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:41.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:41.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:41.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:19:41.885][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:41.888][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:41.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:41.892][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:41.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:41.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:41.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:41.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:41.937][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:19:41.940][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:19:41.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:41.944][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.015][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:19:42.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:19:42.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.025][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:19:42.027][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:19:42.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.031][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.048][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:19:42.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:19:42.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.058][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:42.060][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:42.062][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.065][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.067][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:42.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:42.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.077][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:42.079][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:42.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.084][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:42.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:42.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.096][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:42.098][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:42.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.103][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.106][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:42.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:42.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.115][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:19:42.117][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:42.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.122][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.124][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:19:42.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:42.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.134][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:42.137][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:42.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.142][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.145][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:42.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:42.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.154][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:42.157][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:42.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.162][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.165][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:42.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:42.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.174][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:19:42.177][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:19:42.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.181][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.184][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:19:42.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:19:42.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.193][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:19:42.196][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:19:42.198][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.200][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.202][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:19:42.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:19:42.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:42.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:42.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:42.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:42.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:42.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:42.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:42.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:42.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:42.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:42.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:42.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:42.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:42.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:42.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:19:42.394][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-12-20 00:19:42.400][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:42.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:42.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:42.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:42.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.524][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:42.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:42.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.533][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:42.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:42.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:42.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:42.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:42.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:42.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.561][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-12-20 00:19:42.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-12-20 00:19:42.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.570][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-12-20 00:19:42.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-12-20 00:19:42.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.579][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-12-20 00:19:42.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-12-20 00:19:42.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.588][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-12-20 00:19:42.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-12-20 00:19:42.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:42.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:42.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:42.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:42.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:42.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:42.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:42.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:42.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:42.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:42.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:42.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:42.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:42.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:42.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:42.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:42.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:42.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:42.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:42.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:42.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.833][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:42.836][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:42.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.840][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:42.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:42.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.882][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.902][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.905][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.910][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.912][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:42.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.940][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:42.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:42.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.950][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:42.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:42.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.959][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:42.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:42.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.969][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:42.972][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:42.974][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.976][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:42.979][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:42.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:42.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:42.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.007][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:19:43.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:19:43.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.016][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:19:43.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:19:43.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.026][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:19:43.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:19:43.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.035][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:19:43.037][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:19:43.040][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.042][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.044][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:19:43.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:19:43.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:43.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:43.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:43.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:43.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:43.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:43.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.103][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:43.105][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:43.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.110][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.112][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:43.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:43.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.140][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:43.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:43.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:43.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:43.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:43.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:43.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.179][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:43.182][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:43.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.187][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:43.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:43.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.218][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:19:43.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:19:43.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.229][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:19:43.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:19:43.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.251][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:19:43.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:19:43.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.263][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:19:43.266][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:19:43.268][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.271][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.274][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:19:43.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:19:43.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.308][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-12-20 00:19:43.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:19:43.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.319][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-12-20 00:19:43.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:19:43.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.329][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-12-20 00:19:43.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:19:43.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.338][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-12-20 00:19:43.341][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:19:43.343][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.345][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.348][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-12-20 00:19:43.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:19:43.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.376][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:43.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:43.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.386][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:43.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:43.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.395][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:43.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:43.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.405][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:43.408][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:43.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.413][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.415][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:43.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:43.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.442][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:19:43.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:19:43.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.452][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:19:43.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:19:43.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.462][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:19:43.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:19:43.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.471][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:19:43.474][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:19:43.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.479][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.481][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:19:43.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:19:43.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.511][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:43.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:43.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.521][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:43.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:43.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.531][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:43.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:43.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.540][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:43.542][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:43.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.547][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.549][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:43.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:43.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.576][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:43.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:43.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:43.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:43.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.596][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:43.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:43.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.604][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:43.607][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:43.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.611][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.613][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:43.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:43.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.649][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:43.652][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:43.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.656][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.667][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:19:43.670][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:19:43.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.674][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.685][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:19:43.688][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:19:43.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.693][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.704][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:43.707][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:43.709][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.711][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.722][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:43.724][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:43.727][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.729][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.739][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:43.742][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:43.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.746][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.757][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:43.759][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:43.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.763][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.774][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:43.777][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:43.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.781][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.793][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-12-20 00:19:43.796][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:19:43.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.800][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.812][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:43.814][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:43.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.818][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:43.830][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:19:43.832][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:19:43.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:43.837][ef$get] fields variable is a list.
biodb.INFO [2024-12-20 00:19:43.855][biodb::testThat]
biodb.INFO [2024-12-20 00:19:43.857][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-12-20 00:19:43.859][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:19:43.862][biodb::testThat]
biodb.DEBUG[2024-12-20 00:19:43.898][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-12-20 00:19:43.911][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:19:43.920][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-12-20 00:19:43.923][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:19:43.926][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-12-20 00:19:43.929][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:19:43.993][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:19:43.996][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:19:44.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:19:44.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:44.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:44.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:44.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:44.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:44.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:19:44.037][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:44.040][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:44.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.044][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:44.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:44.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.099][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:19:44.102][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:19:44.105][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.107][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.110][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:19:44.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:19:44.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.120][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:19:44.123][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:19:44.125][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.127][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.130][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:19:44.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:19:44.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.139][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:44.141][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:44.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.146][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.149][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:44.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:44.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.158][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:44.161][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:44.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.165][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.168][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:44.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:44.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.178][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:44.180][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:44.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.185][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.188][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:44.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:44.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.198][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:19:44.200][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:44.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.205][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.208][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:19:44.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:44.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.218][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:44.220][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:44.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.225][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:44.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:44.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.239][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:44.242][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:44.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.246][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.250][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:44.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:44.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.260][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:19:44.263][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:19:44.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.268][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.271][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:19:44.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:19:44.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.282][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:19:44.284][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:19:44.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.289][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.292][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:19:44.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:19:44.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:44.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:44.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:44.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:44.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:44.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:44.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:44.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:44.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:44.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:44.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:44.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:44.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:44.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:44.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:44.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:44.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:44.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:44.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:44.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:44.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:19:44.404][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-12-20 00:19:44.407][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-12-20 00:19:44.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-12-20 00:19:44.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-12-20 00:19:44.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-12-20 00:19:44.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.427][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-12-20 00:19:44.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-12-20 00:19:44.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-12-20 00:19:44.453][biodb::testThat]
biodb.INFO [2024-12-20 00:19:44.455][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-12-20 00:19:44.458][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:19:44.460][biodb::testThat]
biodb.TRACE[2024-12-20 00:19:44.467][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:44.470][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:44.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.475][ef$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:19:44.479][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-12-20 00:19:44.546][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:44.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:44.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.555][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:44.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:44.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:44.563][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:44.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:44.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:44.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:19:44.578][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-12-20 00:19:44.587][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-12-20 00:19:44.640][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:19:44.681][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-12-20 00:19:44.684][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:19:44.688][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-12-20 00:19:44.760][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[2024-12-20 00:19:44.768][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:19:44.770][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:19:44.774][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-12-20 00:19:45.534][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-12-20 00:19:46.135][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:19:46.140][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-12-20 00:19:46.181][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-12-20 00:19:46.187][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-12-20 00:19:46.236][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:46.239][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:46.241][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.243][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.245][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:46.248][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:46.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.252][ef$get] fields variable is a list.
biodb.INFO [2024-12-20 00:19:46.262][biodb::testThat]
biodb.INFO [2024-12-20 00:19:46.264][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-12-20 00:19:46.266][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:19:46.268][biodb::testThat]
biodb.TRACE[2024-12-20 00:19:46.331][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:46.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:46.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.340][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:46.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:46.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.349][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:46.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:46.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:19:46.509][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:19:46.517][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:19:46.520][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-12-20 00:19:46.522][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:19:46.525][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-12-20 00:19:46.563][biodb::testThat]
biodb.INFO [2024-12-20 00:19:46.566][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-12-20 00:19:46.568][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:19:46.570][biodb::testThat]
biodb.TRACE[2024-12-20 00:19:46.619][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:46.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:46.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.629][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:46.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:46.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.639][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:46.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:46.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.648][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:46.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:46.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:46.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:46.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:46.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:46.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.676][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-12-20 00:19:46.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-12-20 00:19:46.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.685][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-12-20 00:19:46.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-12-20 00:19:46.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.694][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-12-20 00:19:46.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-12-20 00:19:46.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.703][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-12-20 00:19:46.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-12-20 00:19:46.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.760][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:46.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:46.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.769][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:46.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:46.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.786][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:46.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:46.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.796][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:46.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:46.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.805][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:46.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:46.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:46.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:46.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.823][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-12-20 00:19:46.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-12-20 00:19:46.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.833][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-12-20 00:19:46.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-12-20 00:19:46.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.841][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-12-20 00:19:46.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-12-20 00:19:46.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:46.851][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-12-20 00:19:46.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-12-20 00:19:46.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:46.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-12-20 00:19:46.873][biodb::testThat]
biodb.INFO [2024-12-20 00:19:46.875][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-12-20 00:19:46.877][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:19:46.879][biodb::testThat]
biodb.INFO [2024-12-20 00:19:46.896][biodb::testThat]
biodb.INFO [2024-12-20 00:19:46.899][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-12-20 00:19:46.901][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:19:46.903][biodb::testThat]
biodb.INFO [2024-12-20 00:19:46.921][biodb::testThat]
biodb.INFO [2024-12-20 00:19:46.924][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-12-20 00:19:46.926][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:19:46.928][biodb::testThat]
biodb.DEBUG[2024-12-20 00:19:46.935][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-12-20 00:19:47.924][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-12-20 00:19:48.932][biodb::testThat]
biodb.INFO [2024-12-20 00:19:48.934][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-12-20 00:19:48.937][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:19:48.939][biodb::testThat]
biodb.DEBUG[2024-12-20 00:19:49.433][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[2024-12-20 00:19:49.894][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:49.896][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:49.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:49.901][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:49.903][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:49.905][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:49.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:49.910][ef$get] fields variable is a list.
biodb.INFO [2024-12-20 00:19:49.914][biodb::testThat]
biodb.INFO [2024-12-20 00:19:49.916][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-12-20 00:19:49.918][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:19:49.920][biodb::testThat]
biodb.TRACE[2024-12-20 00:19:49.947][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:49.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:49.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:49.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:49.957][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:49.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:49.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:49.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:49.966][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:49.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:49.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:49.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:19:50.172][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:19:50.180][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:19:50.183][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-12-20 00:19:50.186][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:19:50.190][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-12-20 00:19:50.352][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:19:50.359][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:19:50.363][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-12-20 00:19:50.366][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:19:50.369][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-12-20 00:19:50.402][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-20 00:19:50.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-20 00:19:50.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:50.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:50.420][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:50.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:50.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:50.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:50.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:50.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:50.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:50.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:50.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:50.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:50.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:50.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:50.450][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:50.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:50.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:50.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:50.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:50.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:50.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:50.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:19:50.484][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:19:50.525][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:19:50.527][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:19:50.578][private$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[2024-12-20 00:19:50.995][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[2024-12-20 00:19:51.404][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:19:51.407][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-12-20 00:19:51.427][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-12-20 00:19:51.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:19:51.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:51.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:51.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:51.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:51.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:51.455][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[2024-12-20 00:19:51.457][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-12-20 00:19:51.583][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:19:51.587][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-12-20 00:19:51.591][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:19:51.593][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:19:51.596][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:19:51.599][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:19:51.615][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:19:51.617][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:19:51.623][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:19:51.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:51.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:51.637][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:51.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:51.642][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:51.644][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[2024-12-20 00:19:51.647][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-12-20 00:19:51.653][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:19:51.656][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:19:51.659][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-12-20 00:19:52.077][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-12-20 00:19:52.479][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:19:52.483][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-12-20 00:19:52.533][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-12-20 00:19:52.539][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-12-20 00:19:52.543][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:19:52.546][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:19:52.549][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:19:52.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:19:52.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:52.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:52.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:52.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:52.572][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:52.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:19:52.579][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:52.582][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:52.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.586][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:52.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:52.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.599][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:19:52.601][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:19:52.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.606][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.609][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:19:52.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:19:52.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.618][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:19:52.621][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:19:52.623][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.625][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.629][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:19:52.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:19:52.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.638][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:52.640][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:52.642][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.645][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.648][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:52.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:52.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.657][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:52.660][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:52.662][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.664][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.667][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:52.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:52.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.677][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:52.679][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:52.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.683][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.686][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:19:52.689][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:52.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.692][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.694][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:19:52.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:52.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.704][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:52.705][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:52.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.709][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.712][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:52.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:52.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.721][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:52.731][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:52.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.741][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.744][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:52.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:52.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.752][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:19:52.754][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:19:52.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.759][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.761][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:19:52.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:19:52.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.769][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:19:52.771][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:19:52.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.776][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.779][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:19:52.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:19:52.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:52.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:52.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.800][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:52.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:52.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:52.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:52.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.820][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:52.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:52.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:52.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:52.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:52.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:52.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:52.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:52.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:52.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:52.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:52.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:52.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:52.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:52.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:19:52.887][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-12-20 00:19:52.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:52.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:52.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.921][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:52.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:52.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:52.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:52.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:52.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:52.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:19:52.942][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[2024-12-20 00:19:52.950][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:19:52.953][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:19:52.957][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-12-20 00:19:53.370][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-12-20 00:19:53.785][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:19:53.789][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-12-20 00:19:53.798][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-12-20 00:19:53.851][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:19:53.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:53.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:53.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:53.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:53.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:53.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:19:53.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:53.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:53.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:53.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:53.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:53.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:53.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:53.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:53.893][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:53.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:53.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:53.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:19:53.903][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:19:53.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:53.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:53.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:53.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:53.919][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:53.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:53.924][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-12-20 00:19:53.927][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:19:53.931][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-12-20 00:19:53.934][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:19:53.936][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:19:53.939][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:19:53.941][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:19:53.943][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:19:53.945][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:19:53.981][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:19:53.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:53.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:53.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:54.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:54.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:54.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:54.007][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-12-20 00:19:54.014][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:19:54.017][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:19:54.020][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-12-20 00:19:54.442][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-12-20 00:19:54.852][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:19:54.857][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-12-20 00:19:54.866][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-12-20 00:19:54.872][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-12-20 00:19:54.877][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:19:54.880][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:19:54.883][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:19:54.887][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:19:54.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:54.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:54.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:54.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:54.922][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:54.924][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.TRACE[2024-12-20 00:19:54.929][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:54.932][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:54.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:54.937][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:54.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:54.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:54.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:54.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:54.950][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:19:54.953][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:19:54.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:54.958][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:54.961][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:19:54.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:19:54.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:54.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:54.971][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:19:54.974][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:19:54.976][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:54.979][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:54.982][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:19:54.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:19:54.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:54.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:54.992][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:54.995][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:54.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.000][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.002][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:55.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:55.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.013][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:55.016][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:55.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.020][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.023][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:55.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:55.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.034][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:55.037][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:55.039][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.041][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.044][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:19:55.047][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:55.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.052][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.055][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:19:55.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:55.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.065][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:55.068][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:55.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.073][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:55.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:55.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.086][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:55.089][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:55.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.094][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.097][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:55.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:55.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.106][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:19:55.108][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:19:55.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.112][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.115][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:19:55.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:19:55.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.125][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:19:55.128][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:19:55.130][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.133][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.136][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:19:55.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:19:55.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.146][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:55.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:55.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:55.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:55.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:55.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:55.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:55.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:55.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:55.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:55.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:55.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:55.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:55.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:55.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:55.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:55.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:55.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:55.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:55.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:55.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:19:55.244][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-12-20 00:19:55.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:55.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:55.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:55.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:55.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:55.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:55.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:19:55.315][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:19:55.323][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:19:55.326][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-12-20 00:19:55.329][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:19:55.332][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-12-20 00:19:55.339][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:19:55.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:55.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:55.356][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:55.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:55.360][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:55.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:19:55.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:55.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:55.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:55.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:55.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:55.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:55.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:55.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:55.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:19:55.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:19:55.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:55.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:55.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:55.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:55.409][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:55.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:55.413][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-12-20 00:19:55.415][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:19:55.419][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-12-20 00:19:55.423][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:19:55.426][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:19:55.428][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:19:55.431][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:19:55.434][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:19:55.435][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:19:55.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:19:55.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:55.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:55.465][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:55.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:55.469][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:55.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:55.474][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-12-20 00:19:55.480][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:19:55.483][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:19:55.486][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-12-20 00:19:55.908][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-12-20 00:19:56.315][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:19:56.320][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-12-20 00:19:56.328][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-12-20 00:19:56.334][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-12-20 00:19:56.338][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:19:56.340][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:19:56.343][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:19:56.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:19:56.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:56.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:56.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:56.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:56.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:56.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:19:56.373][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:56.376][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:56.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.380][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:56.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:56.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.392][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:19:56.395][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:19:56.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.399][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.402][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:19:56.404][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:19:56.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.409][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.412][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:56.414][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:56.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.418][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.421][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:56.424][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:56.426][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.428][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.431][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:56.433][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:56.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.438][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.440][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:19:56.443][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:56.445][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.447][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.450][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:56.453][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:56.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.458][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.461][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:56.464][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:56.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.469][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.472][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:56.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:56.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.482][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:19:56.485][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:19:56.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.489][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.492][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:19:56.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:19:56.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.501][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:19:56.504][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:19:56.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.508][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:56.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:56.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:56.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:56.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:56.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:56.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:56.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:56.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:56.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:56.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:56.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:56.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:56.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:56.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:56.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:56.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:56.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:56.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:56.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:56.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:19:56.615][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-12-20 00:19:56.617][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:56.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:56.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.627][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:56.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:56.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:56.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:56.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:56.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:56.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:56.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:56.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:56.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:56.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:19:56.664][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:19:56.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:56.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:56.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:56.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:56.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:56.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:56.688][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-12-20 00:19:56.690][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:19:56.694][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-12-20 00:19:56.697][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:19:56.700][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:19:56.703][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:19:56.706][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:19:56.708][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:19:56.711][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:19:56.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:19:56.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:56.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:56.733][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:56.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:56.738][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:56.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:56.743][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-12-20 00:19:56.750][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:19:56.752][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:19:56.756][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-12-20 00:19:57.197][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-12-20 00:19:57.607][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:19:57.611][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-12-20 00:19:57.620][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-12-20 00:19:57.627][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-12-20 00:19:57.631][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:19:57.634][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:19:57.637][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:19:57.641][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:19:57.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:57.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:57.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:57.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:57.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:57.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:19:57.683][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:57.686][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:57.688][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.691][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:57.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:57.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.704][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:19:57.707][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:19:57.709][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.711][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.714][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:19:57.717][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:19:57.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.721][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.724][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:57.727][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:57.729][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.731][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.734][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:57.737][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:57.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.741][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.744][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:57.747][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:57.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.751][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.754][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:19:57.757][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:57.759][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.761][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.764][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:57.766][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:57.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.770][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.773][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:57.775][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:57.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.779][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.783][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:57.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:57.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.793][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:19:57.796][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:19:57.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.800][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.803][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:19:57.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:19:57.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.814][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:19:57.817][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:19:57.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.821][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:57.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:57.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:57.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:57.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:57.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:57.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:57.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:57.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:57.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:57.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:57.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:57.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:57.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:57.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:57.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:57.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:57.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:57.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:57.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:57.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:19:57.945][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-12-20 00:19:57.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:57.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:57.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:57.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:57.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.966][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:57.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:57.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:57.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:57.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:57.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:57.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:58.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:58.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:58.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:58.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:19:58.016][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:19:58.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:58.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:58.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:58.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:58.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:58.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:58.041][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-12-20 00:19:58.044][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:19:58.047][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-12-20 00:19:58.050][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:19:58.053][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:19:58.056][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:19:58.058][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:19:58.061][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:19:58.064][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:19:58.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:19:58.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:58.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:58.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:58.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:58.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:58.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:58.096][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-12-20 00:19:58.103][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:19:58.106][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:19:58.110][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-12-20 00:19:58.540][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-12-20 00:19:58.945][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:19:58.951][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-12-20 00:19:58.960][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-12-20 00:19:58.967][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-12-20 00:19:58.970][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:19:58.973][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:19:58.976][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:19:58.980][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:19:58.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:58.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:58.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:58.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:59.000][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:59.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:19:59.007][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:59.009][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:59.010][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.013][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:59.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:59.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.025][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:19:59.028][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:19:59.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.032][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.035][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:19:59.037][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:19:59.040][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.042][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.045][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:19:59.048][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:19:59.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.052][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.055][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:19:59.058][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:19:59.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.070][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.079][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:59.082][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:19:59.084][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.086][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.089][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:19:59.092][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:59.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.096][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.099][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:59.102][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:19:59.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.106][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.109][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:59.112][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:59.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.117][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.121][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:19:59.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:19:59.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.131][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:19:59.133][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:19:59.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.138][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.141][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:19:59.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:19:59.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.151][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:19:59.153][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:19:59.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.158][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:59.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:59.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:59.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:59.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:59.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:59.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:19:59.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:19:59.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:59.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:59.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:59.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:59.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:59.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:59.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:59.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:59.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:59.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:59.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:19:59.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:19:59.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:19:59.288][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-12-20 00:19:59.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:59.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:59.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:59.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:59.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:59.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:59.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:59.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:59.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:19:59.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:59.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:19:59.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:19:59.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:19:59.344][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:19:59.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:59.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:59.358][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:59.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:59.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:59.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:59.367][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-12-20 00:19:59.369][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:19:59.373][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-12-20 00:19:59.385][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:19:59.387][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:19:59.390][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:19:59.393][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:19:59.396][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:19:59.398][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:19:59.404][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:19:59.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:19:59.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:19:59.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:19:59.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:19:59.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:19:59.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:19:59.428][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-12-20 00:19:59.434][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:19:59.436][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:19:59.439][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-12-20 00:19:59.886][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-12-20 00:20:00.313][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:00.317][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-12-20 00:20:00.325][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-12-20 00:20:00.332][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-12-20 00:20:00.335][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:20:00.339][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:20:00.341][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:20:00.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:00.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:00.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:00.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:00.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:00.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:00.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:00.373][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:00.375][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:00.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.379][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:00.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:00.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.391][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:00.394][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:00.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.398][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.401][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:00.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:00.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.411][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:00.413][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:00.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.417][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.420][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:00.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:00.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.429][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:00.432][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:00.434][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.436][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.437][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:00.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:00.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.445][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:00.448][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:00.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.452][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.454][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:00.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:00.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.464][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:00.467][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:00.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.472][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.475][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:00.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:00.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.485][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:00.487][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:00.489][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.492][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.494][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:00.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:00.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.504][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:00.506][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:00.517][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.525][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:00.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:00.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.539][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:00.542][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:00.544][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.546][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.550][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:00.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:00.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.561][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:00.564][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:00.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.568][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.571][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:00.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:00.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.581][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:00.583][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:00.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.588][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.591][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:00.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:00.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:00.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:00.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:00.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:00.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:00.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:00.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:00.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:00.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:00.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:00.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:00.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:00.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:00.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:00.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:00.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:00.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:00.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:00.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:00.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:00.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:00.697][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-12-20 00:20:00.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:00.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:00.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:00.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:00.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:00.715][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:00.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:00.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:00.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:00.724][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:00.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:00.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:00.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:00.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:00.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:00.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:00.749][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-12-20 00:20:00.752][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:20:00.756][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-12-20 00:20:00.759][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:20:00.762][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:20:00.764][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:20:00.767][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:00.769][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:20:00.771][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:20:00.777][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:00.779][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:00.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:00.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:00.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:00.805][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:00.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:00.810][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-12-20 00:20:00.816][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:00.819][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:00.822][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-12-20 00:20:01.275][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-12-20 00:20:01.700][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:01.705][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-12-20 00:20:01.713][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-12-20 00:20:01.720][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-12-20 00:20:01.724][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:20:01.727][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:20:01.730][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:20:01.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:01.736][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:01.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:01.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:01.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:01.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:01.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:01.761][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:01.764][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:01.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.768][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:01.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:01.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.778][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:01.780][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:01.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.785][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.788][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:01.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:01.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.797][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:01.798][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:01.800][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.801][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.803][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:01.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:01.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.811][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:01.814][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:01.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.819][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.822][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:01.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:01.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.832][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:01.835][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:01.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.840][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.843][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:01.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:01.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.852][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:01.854][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:01.856][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.858][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.861][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:01.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:01.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.871][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:01.874][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:01.876][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.879][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.882][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:01.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:01.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.891][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:01.893][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:01.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.896][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:01.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:01.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.908][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:01.911][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:01.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.915][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.918][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:01.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:01.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.941][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:01.943][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:01.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.948][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.951][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:01.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:01.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.961][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:01.963][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:01.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.967][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.970][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:01.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:01.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:01.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:01.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:01.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:01.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:01.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:01.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:02.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:02.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:02.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:02.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:02.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:02.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:02.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:02.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:02.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:02.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:02.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:02.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:02.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:02.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:02.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:02.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:02.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:02.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:02.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:02.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:02.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:02.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:02.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:02.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:02.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:02.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:02.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:02.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:02.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:02.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:02.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:02.071][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-12-20 00:20:02.073][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:02.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:02.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:02.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:02.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:02.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:02.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:02.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:02.091][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:02.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:02.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:02.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:02.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:02.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:02.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:02.115][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:02.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:02.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:02.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:02.125][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-12-20 00:20:02.127][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:20:02.131][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-12-20 00:20:02.133][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:20:02.136][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:20:02.138][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:20:02.141][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:02.143][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:20:02.145][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:20:02.150][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:02.152][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:02.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:02.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:02.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:02.169][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:02.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:02.174][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-12-20 00:20:02.180][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:02.183][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:02.194][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-12-20 00:20:02.615][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-12-20 00:20:03.027][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:03.031][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-12-20 00:20:03.039][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-12-20 00:20:03.045][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-12-20 00:20:03.049][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:20:03.052][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:20:03.055][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:20:03.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:03.059][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:03.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:03.072][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:03.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:03.077][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:03.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:03.084][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:03.087][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:03.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.091][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:03.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:03.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.101][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:03.104][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:03.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.108][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.110][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:03.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:03.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.120][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:03.122][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:03.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.126][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.129][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:03.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:03.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.139][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:03.141][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:03.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.146][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.149][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:03.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:03.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.159][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:03.162][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:03.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.166][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.169][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:03.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:03.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.178][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:03.181][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:03.183][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.185][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.187][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:03.189][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:03.190][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.191][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.193][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:03.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:03.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.199][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:03.202][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:03.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.206][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:03.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:03.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.219][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:03.221][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:03.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.226][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.229][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:03.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:03.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.239][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:03.242][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:03.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.246][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.249][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:03.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:03.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.259][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:03.261][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:03.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.276][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.278][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:03.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:03.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:03.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:03.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:03.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:03.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:03.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:03.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:03.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:03.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:03.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:03.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:03.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:03.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:03.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:03.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:03.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:03.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:03.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:03.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:03.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:03.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:03.366][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-12-20 00:20:03.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:03.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:03.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.376][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:03.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:03.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:03.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:03.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:03.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:03.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:03.388][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:03.389][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:03.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:03.399][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:03.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:03.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:03.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:03.404][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-12-20 00:20:03.407][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:20:03.410][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-12-20 00:20:03.413][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:20:03.415][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:20:03.416][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:20:03.417][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:03.420][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:20:03.422][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:20:03.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:03.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:03.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:03.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:03.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:03.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:03.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:03.451][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-12-20 00:20:03.458][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:03.460][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:03.463][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-12-20 00:20:03.892][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-12-20 00:20:04.306][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:04.311][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-12-20 00:20:04.317][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-12-20 00:20:04.323][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-12-20 00:20:04.327][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:20:04.330][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:20:04.346][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:20:04.350][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:04.352][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:04.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:04.366][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:04.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:04.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:04.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:04.376][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:04.379][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:04.381][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.383][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:04.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:04.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.396][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:04.399][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:04.401][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.404][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.407][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:04.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:04.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.416][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:04.419][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:04.421][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.423][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.426][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:04.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:04.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.436][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:04.438][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:04.440][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.442][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.445][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:04.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:04.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.454][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:04.456][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:04.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.460][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.463][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:04.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:04.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.471][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:04.473][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:04.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.478][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.480][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:04.482][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:04.484][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.486][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.489][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:04.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:04.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.499][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:04.501][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:04.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.506][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:04.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:04.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.518][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:04.521][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:04.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.525][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.528][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:04.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:04.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.539][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:04.541][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:04.544][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.546][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.549][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:04.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:04.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.560][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:04.563][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:04.565][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.567][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.570][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:04.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:04.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:04.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:04.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:04.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:04.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:04.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:04.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:04.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:04.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:04.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:04.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:04.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:04.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:04.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:04.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:04.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:04.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:04.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:04.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:04.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:04.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:04.680][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-12-20 00:20:04.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:04.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:04.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.692][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:04.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:04.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:04.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:04.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:04.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:04.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:04.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:04.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:04.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:04.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:04.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:04.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:04.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:04.733][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-12-20 00:20:04.736][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:20:04.738][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-12-20 00:20:04.741][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:20:04.744][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:20:04.746][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:20:04.748][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:04.751][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:20:04.753][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:20:04.758][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:04.760][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:04.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:04.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:04.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:04.777][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:04.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:04.781][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-12-20 00:20:04.787][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:04.790][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:04.792][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-12-20 00:20:05.233][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-12-20 00:20:05.636][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:05.640][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-12-20 00:20:05.648][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-12-20 00:20:05.655][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-12-20 00:20:05.659][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:20:05.662][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:20:05.664][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:20:05.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:05.670][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:05.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:05.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:05.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:05.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:05.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:05.703][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:05.711][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:05.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.716][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:05.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:05.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.729][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:05.732][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:05.734][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.736][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.739][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:05.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:05.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.749][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:05.751][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:05.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.755][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.756][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:05.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:05.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.766][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:05.768][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:05.770][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.772][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.775][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:05.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:05.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.783][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:05.786][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:05.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.789][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.792][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:05.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:05.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.801][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:05.803][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:05.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.807][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.810][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:05.812][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:05.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.816][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.819][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:05.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:05.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.828][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:05.831][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:05.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.836][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:05.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:05.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.846][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:05.849][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:05.851][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.852][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.855][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:05.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:05.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.864][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:05.866][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:05.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.870][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.873][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:05.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:05.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.882][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:05.884][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:05.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.889][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.892][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:05.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:05.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.902][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:05.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:05.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.911][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:05.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:05.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:05.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:05.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:05.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:05.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:05.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:05.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:05.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:05.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:05.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:05.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:05.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:05.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:05.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:05.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:05.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:05.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:05.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:05.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:05.998][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-12-20 00:20:06.001][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:06.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:06.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:06.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:06.010][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:06.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:06.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:06.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:06.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:06.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:06.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:06.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:06.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:06.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:06.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:06.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:06.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:06.047][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:06.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:06.051][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-12-20 00:20:06.053][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:20:06.057][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-12-20 00:20:06.060][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:20:06.063][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:20:06.065][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:20:06.068][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:06.070][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:20:06.072][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:20:06.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:06.081][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:06.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:06.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:06.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:06.099][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:06.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:06.103][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-12-20 00:20:06.110][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:06.112][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:06.116][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-12-20 00:20:06.550][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-12-20 00:20:06.955][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:06.960][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-12-20 00:20:06.968][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-12-20 00:20:06.975][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-12-20 00:20:06.978][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:20:06.981][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:20:06.983][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:20:06.987][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:06.989][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:06.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:07.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:07.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:07.007][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:07.009][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.TRACE[2024-12-20 00:20:07.014][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:07.017][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:07.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.021][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:07.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:07.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.033][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:07.035][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:07.037][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.039][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.042][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:07.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:07.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.065][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:07.068][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:07.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.072][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.075][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:07.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:07.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.085][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:07.087][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:07.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.092][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.094][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:07.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:07.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.104][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:07.106][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:07.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.110][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.113][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:07.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:07.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.122][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:07.124][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:07.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.128][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.131][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:07.133][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:07.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.138][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.140][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:07.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:07.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.150][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:07.153][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:07.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.158][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:07.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:07.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.171][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:07.173][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:07.175][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.177][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.180][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:07.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:07.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.190][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:07.192][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:07.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.196][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.199][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:07.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:07.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.208][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:07.211][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:07.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.215][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.218][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:07.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:07.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:07.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:07.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:07.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:07.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:07.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:07.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:07.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:07.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:07.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:07.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:07.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:07.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:07.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:07.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:07.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:07.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:07.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:07.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:07.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:07.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:07.308][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-12-20 00:20:07.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:07.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:07.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:07.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:07.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:07.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:07.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:07.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:07.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:07.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:07.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:07.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:07.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:07.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:07.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:07.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:07.360][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-12-20 00:20:07.362][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:20:07.366][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-12-20 00:20:07.369][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:20:07.372][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:20:07.374][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:20:07.377][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:07.379][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:20:07.382][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:20:07.388][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:07.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:07.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:07.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:07.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:07.408][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:07.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:07.413][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-12-20 00:20:07.420][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:07.422][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:07.425][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-12-20 00:20:07.849][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-12-20 00:20:08.266][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:08.271][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-12-20 00:20:08.280][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-12-20 00:20:08.286][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-12-20 00:20:08.290][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:20:08.293][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:20:08.296][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:20:08.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:08.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:08.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:08.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:08.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:08.321][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:08.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:08.329][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:08.332][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:08.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.337][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:08.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:08.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.350][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:08.353][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:08.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.358][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.361][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:08.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:08.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.372][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:08.374][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:08.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.379][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.382][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:08.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:08.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.393][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:08.409][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:08.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.415][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.418][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:08.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:08.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.428][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:08.430][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:08.432][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.435][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.438][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:08.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:08.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.448][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:08.450][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:08.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.455][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.458][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:08.460][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:08.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.465][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.468][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:08.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:08.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.478][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:08.481][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:08.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.485][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:08.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:08.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.499][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:08.501][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:08.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.506][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.510][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:08.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:08.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.519][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:08.522][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:08.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.527][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.530][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:08.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:08.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.540][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:08.543][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:08.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.547][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.550][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:08.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:08.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.561][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:08.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:08.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:08.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:08.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:08.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:08.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:08.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:08.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:08.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:08.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:08.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:08.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:08.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:08.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:08.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:08.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:08.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:08.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:08.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:08.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:08.654][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-12-20 00:20:08.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:08.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:08.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:08.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:08.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:08.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:08.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:08.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:08.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:08.692][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:08.694][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:08.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:08.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:08.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:08.712][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:08.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:08.716][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-12-20 00:20:08.719][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:20:08.722][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-12-20 00:20:08.725][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:20:08.727][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:20:08.730][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:20:08.732][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:08.734][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:20:08.737][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:20:08.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:08.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:08.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:08.758][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:08.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:08.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:08.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:08.767][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-12-20 00:20:08.773][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:08.775][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:08.779][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-12-20 00:20:09.209][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-12-20 00:20:09.632][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:09.637][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-12-20 00:20:09.645][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-12-20 00:20:09.651][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-12-20 00:20:09.654][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:20:09.657][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:20:09.660][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:20:09.664][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:09.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:09.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:09.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:09.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:09.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:09.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:09.690][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:09.692][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:09.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.696][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:09.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:09.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.708][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:09.710][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:09.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.715][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.718][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:09.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:09.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.727][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:09.729][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:09.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.733][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.736][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:09.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:09.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.745][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:09.747][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:09.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.751][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.754][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:09.756][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:09.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.761][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.763][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:09.765][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:09.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.769][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.784][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:09.787][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:09.789][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.791][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.794][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:09.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:09.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.803][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:09.805][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:09.808][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.810][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:09.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:09.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.822][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:09.824][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:09.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.828][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.830][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:09.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:09.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.838][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:09.840][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:09.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.843][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.846][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:09.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:09.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.854][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:09.857][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:09.859][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.861][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:09.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:09.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:09.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:09.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:09.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:09.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:09.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:09.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:09.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:09.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:09.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:09.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:09.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:09.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:09.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:09.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:09.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:09.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:09.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:09.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:09.951][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-12-20 00:20:09.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:09.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:09.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.963][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:09.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:09.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:09.972][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:09.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:09.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:09.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:09.980][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:09.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:09.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:09.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:09.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:09.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:10.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:10.003][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-12-20 00:20:10.005][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:20:10.009][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-12-20 00:20:10.011][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:20:10.014][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:20:10.024][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:20:10.027][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:10.030][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:20:10.032][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:20:10.038][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:10.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:10.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:10.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:10.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:10.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:10.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:10.062][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-12-20 00:20:10.069][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:10.071][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:10.075][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-12-20 00:20:10.533][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-12-20 00:20:10.939][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:10.943][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-12-20 00:20:10.950][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-12-20 00:20:10.956][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-12-20 00:20:10.960][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:20:10.963][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:20:10.965][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:20:10.969][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:10.971][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:10.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:10.984][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:10.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:10.988][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:10.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:10.995][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:10.998][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:11.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.003][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:11.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:11.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.015][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:11.017][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:11.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.022][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.024][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:11.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:11.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.034][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:11.036][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:11.038][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.040][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.042][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:11.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:11.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.051][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:11.053][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:11.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.057][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.059][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:11.062][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:11.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.066][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.069][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:11.071][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:11.073][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.075][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.078][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:11.080][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:11.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.084][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.087][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:11.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:11.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.096][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:11.099][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:11.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.103][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:11.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:11.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.113][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:11.115][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:11.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.119][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.122][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:11.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:11.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.145][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:11.147][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:11.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.152][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.155][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:11.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:11.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.165][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:11.167][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:11.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.171][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:11.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:11.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:11.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:11.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:11.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:11.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:11.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:11.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:11.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:11.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:11.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:11.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:11.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:11.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:11.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:11.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:11.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:11.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:11.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:11.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:11.257][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-12-20 00:20:11.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:11.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:11.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:11.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:11.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:11.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:11.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:11.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:11.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:11.281][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:11.283][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:11.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:11.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:11.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:11.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:11.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:11.300][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-12-20 00:20:11.302][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:20:11.306][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-12-20 00:20:11.308][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:20:11.310][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:20:11.312][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:20:11.315][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:11.317][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:20:11.319][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:20:11.324][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:11.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:11.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:11.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:11.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:11.344][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:11.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:11.349][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-12-20 00:20:11.354][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:11.356][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:11.359][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-12-20 00:20:11.996][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-12-20 00:20:12.416][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:12.420][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-12-20 00:20:12.428][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-12-20 00:20:12.434][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-12-20 00:20:12.438][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:20:12.442][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:20:12.444][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:20:12.448][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:12.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:12.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:12.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:12.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:12.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:12.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:12.476][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:12.479][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:12.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.484][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:12.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:12.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.495][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:12.498][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:12.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.502][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.505][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:12.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:12.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.515][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:12.517][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:12.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.521][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.524][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:12.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:12.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.533][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:12.535][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:12.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.540][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.543][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:12.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:12.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.552][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:12.555][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:12.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.559][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.562][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:12.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:12.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.571][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:12.574][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:12.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.578][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.581][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:12.583][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:12.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.586][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.589][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:12.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:12.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.599][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:12.601][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:12.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.606][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:12.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:12.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.617][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:12.620][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:12.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.624][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.627][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:12.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:12.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.634][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:12.636][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:12.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.639][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.641][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:12.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:12.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.651][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:12.653][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:12.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.657][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.671][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:12.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:12.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:12.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:12.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.689][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:12.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:12.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:12.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:12.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.706][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:12.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:12.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:12.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:12.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:12.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:12.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:12.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:12.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:12.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:12.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:12.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:12.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:12.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:12.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:12.764][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-12-20 00:20:12.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:12.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:12.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:12.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:12.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:12.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:12.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:12.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:12.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:12.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:12.793][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:12.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:12.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:12.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:12.811][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:12.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:12.816][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-12-20 00:20:12.818][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:20:12.822][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-12-20 00:20:12.825][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:20:12.827][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:20:12.830][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:20:12.833][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:12.834][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:20:12.835][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:20:12.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:12.841][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:12.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:12.854][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:12.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:12.858][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:12.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:12.862][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-12-20 00:20:12.868][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:12.870][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:12.874][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-12-20 00:20:13.297][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-12-20 00:20:13.725][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:13.729][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-12-20 00:20:13.737][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-12-20 00:20:13.744][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-12-20 00:20:13.759][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:20:13.768][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:20:13.771][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:20:13.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:13.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:13.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:13.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:13.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:13.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:13.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:13.802][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:13.805][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:13.806][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:13.808][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:13.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:13.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:13.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:13.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:13.820][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:13.823][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:13.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:13.828][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:13.831][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:13.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:13.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:13.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:13.842][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:13.844][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:13.847][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:13.849][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:13.852][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:13.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:13.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:13.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:13.862][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:13.864][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:13.866][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:13.868][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:13.870][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:13.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:13.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:13.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:13.879][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:13.881][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:13.883][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:13.884][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:13.886][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:13.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:13.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:13.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:13.895][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:13.898][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:13.900][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:13.902][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:13.905][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:13.907][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:13.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:13.912][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:13.914][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:13.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:13.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:13.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:13.924][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:13.926][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:13.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:13.930][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:13.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:13.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:13.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:13.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:13.943][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:13.945][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:13.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:13.950][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:13.953][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:13.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:13.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:13.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:13.962][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:13.964][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:13.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:13.969][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:13.971][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:13.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:13.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:13.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:13.980][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:13.982][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:13.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:13.986][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:13.989][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:13.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:13.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:13.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:13.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:14.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:14.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:14.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:14.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:14.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:14.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:14.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:14.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:14.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:14.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:14.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:14.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:14.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:14.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:14.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:14.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:14.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:14.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:14.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:14.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:14.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:14.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:14.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:14.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:14.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:14.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:14.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:14.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:14.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:14.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:14.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:14.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:14.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:14.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:14.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:14.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:14.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:14.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:14.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:14.099][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-12-20 00:20:14.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:14.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:14.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:14.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:14.113][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:14.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:14.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:14.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:14.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:14.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:14.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:14.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:14.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:14.135][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:14.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:14.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:14.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:14.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:14.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:14.157][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-12-20 00:20:14.159][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:20:14.162][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-12-20 00:20:14.165][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:20:14.168][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:20:14.171][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:20:14.173][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:14.176][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:20:14.178][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:20:14.183][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:14.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:14.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:14.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:14.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:14.203][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:14.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:14.209][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-12-20 00:20:14.215][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:14.217][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:14.221][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-12-20 00:20:14.672][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-12-20 00:20:15.112][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:15.117][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-12-20 00:20:15.125][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-12-20 00:20:15.132][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-12-20 00:20:15.135][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:20:15.138][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:20:15.140][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:20:15.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:15.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:15.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:15.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:15.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:15.162][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:15.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:15.178][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:15.181][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:15.183][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.185][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:15.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:15.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.197][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:15.200][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:15.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.202][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.205][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:15.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:15.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.211][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:15.213][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:15.214][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.216][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.218][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:15.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:15.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.227][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:15.229][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:15.230][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.232][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.235][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:15.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:15.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.243][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:15.245][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:15.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.250][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.252][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:15.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:15.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.262][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:15.265][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:15.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.268][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.271][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:15.273][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:15.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.278][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.281][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:15.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:15.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.290][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:15.293][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:15.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.296][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:15.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:15.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.308][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:15.310][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:15.312][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.314][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.317][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:15.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:15.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.326][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:15.328][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:15.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.333][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.335][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:15.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:15.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.344][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:15.347][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:15.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.349][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.352][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:15.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:15.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:15.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:15.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:15.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:15.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:15.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:15.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:15.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:15.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:15.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:15.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:15.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:15.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:15.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:15.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:15.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:15.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:15.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:15.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:15.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:15.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:15.459][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-12-20 00:20:15.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:15.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:15.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.470][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:15.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:15.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:15.480][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:15.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:15.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:15.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:15.489][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:15.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:15.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:15.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:15.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:15.509][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:15.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:15.513][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-12-20 00:20:15.516][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:20:15.520][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-12-20 00:20:15.523][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:20:15.526][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:20:15.529][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:20:15.531][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:15.534][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:20:15.536][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:20:15.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:15.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:15.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:15.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:15.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:15.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:15.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:15.570][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-12-20 00:20:15.577][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:15.580][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:15.583][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-12-20 00:20:16.021][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-12-20 00:20:16.434][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:16.439][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-12-20 00:20:16.447][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-12-20 00:20:16.452][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-12-20 00:20:16.455][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:20:16.458][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:20:16.461][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:20:16.464][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:16.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:16.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:16.478][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:16.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:16.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:16.483][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.TRACE[2024-12-20 00:20:16.487][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:16.490][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:16.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.494][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:16.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:16.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.506][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:16.508][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:16.510][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.525][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.528][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:16.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:16.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.537][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:16.540][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:16.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.544][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.546][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:16.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:16.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.556][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:16.559][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:16.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.564][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.566][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:16.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:16.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.576][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:16.578][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:16.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.582][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:16.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:16.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.596][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:16.598][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:16.601][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.603][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.606][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:16.609][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:16.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.614][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.616][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:16.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:16.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.628][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:16.631][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:16.633][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.636][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:16.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:16.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.650][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:16.652][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:16.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.657][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.659][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:16.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:16.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.668][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:16.670][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:16.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.673][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.676][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:16.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:16.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.686][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:16.688][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:16.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.692][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.695][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:16.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:16.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.704][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:16.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:16.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:16.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:16.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:16.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:16.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.732][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:16.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:16.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:16.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:16.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:16.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:16.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:16.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:16.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:16.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:16.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:16.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:16.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:16.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:16.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:16.799][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-12-20 00:20:16.800][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:16.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:16.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.809][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:16.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:16.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:16.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:16.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:16.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:16.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:16.824][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:16.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:16.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:16.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:16.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:16.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:16.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:16.846][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-12-20 00:20:16.848][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:20:16.852][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-12-20 00:20:16.854][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:20:16.856][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:20:16.858][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:20:16.859][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:16.860][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:20:16.862][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:20:16.865][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:16.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:16.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:16.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:16.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:16.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:16.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:16.881][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-12-20 00:20:16.888][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:16.890][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:16.893][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-12-20 00:20:17.313][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-12-20 00:20:17.748][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:17.752][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-12-20 00:20:17.761][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-12-20 00:20:17.767][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-12-20 00:20:17.771][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:20:17.774][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:20:17.777][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:20:17.781][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:17.783][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:17.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:17.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:17.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:17.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:17.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:17.807][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:17.810][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:17.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:17.814][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:17.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:17.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:17.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:17.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:17.825][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:17.827][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:17.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:17.831][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:17.834][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:17.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:17.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:17.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:17.844][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:17.847][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:17.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:17.851][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:17.854][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:17.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:17.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:17.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:17.879][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:17.882][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:17.885][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:17.887][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:17.890][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:17.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:17.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:17.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:17.900][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:17.903][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:17.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:17.908][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:17.911][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:17.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:17.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:17.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:17.921][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:17.924][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:17.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:17.928][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:17.931][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:17.934][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:17.937][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:17.939][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:17.942][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:17.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:17.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:17.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:17.953][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:17.956][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:17.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:17.961][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:17.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:17.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:17.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:17.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:17.975][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:17.978][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:17.980][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:17.983][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:17.986][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:17.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:17.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:17.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:17.997][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:17.999][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:18.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:18.004][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:18.007][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:18.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:18.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:18.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:18.017][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:18.020][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:18.022][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:18.024][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:18.026][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:18.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:18.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:18.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:18.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:18.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:18.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:18.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:18.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:18.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:18.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:18.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:18.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:18.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:18.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:18.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:18.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:18.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:18.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:18.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:18.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:18.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:18.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:18.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:18.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:18.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:18.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:18.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:18.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:18.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:18.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:18.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:18.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:18.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:18.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:18.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:18.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:18.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:18.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:18.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:18.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:18.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:18.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:18.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:18.130][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-12-20 00:20:18.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:18.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:18.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:18.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:18.151][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:18.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:18.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:18.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:18.159][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:18.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:18.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:18.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:18.169][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:18.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:18.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:18.184][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:18.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:18.188][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:18.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:18.193][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-12-20 00:20:18.196][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:20:18.200][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-12-20 00:20:18.203][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:20:18.205][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:20:18.208][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:20:18.210][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:18.212][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:20:18.215][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:20:18.221][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:18.223][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:18.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:18.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:18.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:18.240][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:18.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:18.245][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-12-20 00:20:18.252][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:18.254][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:18.257][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-12-20 00:20:18.699][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-12-20 00:20:19.117][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:19.121][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-12-20 00:20:19.130][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-12-20 00:20:19.137][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-12-20 00:20:19.140][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:20:19.144][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:20:19.147][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:20:19.151][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:19.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:19.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:19.166][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:19.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:19.171][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:19.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:19.178][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:19.182][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:19.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.186][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:19.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:19.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.201][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:19.203][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:19.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.208][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.212][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:19.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:19.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.223][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:19.226][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:19.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.230][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.234][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:19.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:19.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.245][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:19.248][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:19.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.253][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.255][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:19.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:19.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.264][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:19.279][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:19.281][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.282][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.285][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:19.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:19.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.295][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:19.297][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:19.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.301][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.304][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:19.307][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:19.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.311][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.312][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:19.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:19.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.318][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:19.319][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:19.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.322][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.324][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:19.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:19.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.330][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:19.331][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:19.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.335][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.338][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:19.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:19.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.348][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:19.350][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:19.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.354][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.357][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:19.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:19.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.367][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:19.369][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:19.372][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.374][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.377][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:19.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:19.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:19.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:19.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:19.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:19.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:19.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:19.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:19.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:19.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:19.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:19.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:19.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:19.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:19.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:19.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:19.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:19.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:19.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:19.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:19.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:19.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:19.480][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-12-20 00:20:19.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:19.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:19.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:19.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:19.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:19.501][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:19.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:19.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:19.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:19.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:19.521][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:19.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:19.535][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:19.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:19.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:19.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:19.544][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-12-20 00:20:19.546][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:20:19.550][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-12-20 00:20:19.553][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:20:19.555][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:20:19.557][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:20:19.560][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:19.562][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:20:19.564][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:20:19.570][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:19.572][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:19.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:19.585][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:19.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:19.590][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:19.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:19.595][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-12-20 00:20:19.600][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:19.602][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:19.605][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-12-20 00:20:20.036][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-12-20 00:20:20.450][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:20.455][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-12-20 00:20:20.499][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-12-20 00:20:20.505][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-12-20 00:20:20.509][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:20:20.511][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:20:20.514][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:20:20.518][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:20.521][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:20.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:20.534][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:20.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:20.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:20.540][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[2024-12-20 00:20:20.545][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:20.548][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:20.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.552][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:20.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:20.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.564][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:20.567][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:20.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.572][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.575][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:20.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:20.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.585][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:20.587][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:20.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.592][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.596][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:20.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:20.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.606][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:20.608][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:20.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.612][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.614][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:20.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:20.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.625][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:20.627][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:20.630][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.632][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.635][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:20.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:20.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.646][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:20.648][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:20.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.666][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.670][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:20.674][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:20.677][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.679][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.683][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:20.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:20.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.694][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:20.697][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:20.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.703][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:20.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:20.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.716][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:20.719][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:20.722][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.725][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.729][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:20.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:20.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.740][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:20.743][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:20.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.748][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.751][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:20.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:20.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.761][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:20.763][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:20.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.768][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.771][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:20.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:20.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.781][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:20.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:20.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:20.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:20.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:20.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:20.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:20.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:20.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:20.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:20.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:20.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:20.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:20.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:20.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:20.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:20.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:20.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:20.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:20.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:20.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:20.880][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-12-20 00:20:20.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:20.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:20.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.893][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:20.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:20.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:20.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:20.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:20.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:20.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:20.964][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:20.972][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:20:20.975][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-12-20 00:20:20.978][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:20:20.981][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-12-20 00:20:20.988][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:20.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:20.992][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:21.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:21.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:21.007][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:21.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:21.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.020][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.030][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:21.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:21.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:21.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:21.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:21.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:21.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:21.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:21.064][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:21.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:21.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:21.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:21.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:21.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:21.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:21.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:21.134][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.164][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:21.183][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:21.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:21.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:21.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:21.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:21.203][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:21.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:21.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.226][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.244][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:21.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:21.262][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:21.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:21.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:21.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:21.280][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:21.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:21.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:21.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:21.312][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:21.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:21.326][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:21.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:21.330][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:21.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:21.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.344][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:21.362][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:21.364][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:21.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:21.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:21.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:21.382][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:21.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:21.387][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.408][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:21.417][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:21.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:21.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:21.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:21.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:21.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:21.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:21.445][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:21.483][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:21.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:21.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:21.499][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:21.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:21.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:21.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:21.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:21.536][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:21.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:21.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:21.552][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:21.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:21.556][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:21.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:21.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.580][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:21.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:21.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:21.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:21.607][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:21.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:21.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:21.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:21.617][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.627][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:21.645][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:21.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:21.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:21.661][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:21.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:21.666][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:21.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:21.671][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.690][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:21.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:21.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:21.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:21.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:21.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:21.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:21.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:21.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.754][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:21.764][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:21.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:21.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:21.779][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:21.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:21.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:21.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:21.788][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:21.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:21.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:21.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:21.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:21.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:21.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:21.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:21.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.858][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:21.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:21.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:21.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:21.883][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:21.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:21.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:21.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:21.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.910][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:21.918][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:21.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:21.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:21.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:21.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:21.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:21.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:21.941][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:21.959][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:21.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:21.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:21.968][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:21.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:21.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:21.984][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:21.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:21.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:21.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:21.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:22.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:22.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:22.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:22.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:22.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:22.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:22.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:22.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:22.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:22.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:22.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:22.031][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:22.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:22.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:22.047][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:22.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:22.051][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:22.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:22.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:22.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:22.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:22.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:22.065][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:22.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:22.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:22.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:22.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:22.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:22.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:22.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:22.084][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:22.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:22.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:22.099][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:22.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:22.104][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:22.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:22.109][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:22.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:22.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:22.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:22.119][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:22.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:22.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:22.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:22.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:22.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:22.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:22.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:22.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:22.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:22.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:22.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:22.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:22.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:22.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:22.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:22.195][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:22.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:22.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:22.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:22.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:22.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:22.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:22.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:22.216][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:22.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:22.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:22.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:22.307][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:22.316][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:22.318][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:22.323][private$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[2024-12-20 00:20:22.735][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[2024-12-20 00:20:23.145][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:23.149][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-12-20 00:20:23.159][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-12-20 00:20:23.167][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[2024-12-20 00:20:23.176][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:23.178][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:23.183][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-12-20 00:20:23.599][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-12-20 00:20:24.011][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:24.016][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-12-20 00:20:24.025][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-12-20 00:20:24.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:24.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:24.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:24.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:24.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:24.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:24.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:24.057][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-12-20 00:20:24.059][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:20:24.063][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-12-20 00:20:24.066][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:20:24.069][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:20:24.071][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:20:24.074][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:24.076][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:20:24.078][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:20:24.084][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:24.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:24.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:24.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:24.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:24.104][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:24.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:24.109][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-12-20 00:20:24.116][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:24.119][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:24.124][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-12-20 00:20:24.553][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-12-20 00:20:24.974][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:24.979][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-12-20 00:20:24.987][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-12-20 00:20:24.993][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-12-20 00:20:24.997][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:20:25.000][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:20:25.002][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:20:25.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:25.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:25.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:25.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:25.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:25.049][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:25.051][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.TRACE[2024-12-20 00:20:25.056][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:25.058][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:25.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.063][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:25.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:25.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.075][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:25.078][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:25.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.082][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.085][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:25.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:25.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.094][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:25.097][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:25.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.101][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.104][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:25.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:25.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.114][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:25.116][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:25.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.120][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.123][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:25.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:25.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.133][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:25.135][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:25.137][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.139][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.142][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:25.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:25.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.151][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:25.154][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:25.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.158][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.161][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:25.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:25.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.171][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:25.173][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:25.175][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.177][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.180][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:25.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:25.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.190][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:25.194][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:25.196][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.199][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:25.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:25.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.211][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:25.214][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:25.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.230][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.234][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:25.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:25.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.246][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:25.250][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:25.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.255][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.258][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:25.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:25.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.268][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:25.271][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:25.273][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.275][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.278][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:25.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:25.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:25.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:25.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:25.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:25.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:25.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:25.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:25.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:25.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:25.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:25.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:25.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:25.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:25.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:25.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:25.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:25.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:25.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:25.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:25.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:25.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:25.399][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-12-20 00:20:25.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:25.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:25.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:25.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:25.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:25.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:25.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:25.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:25.433][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:25.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:25.446][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:25.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:25.452][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:25.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:25.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:25.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:25.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:25.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:25.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:25.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:25.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:25.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:25.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:25.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:25.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:25.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:25.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:25.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:25.511][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:25.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:25.516][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-12-20 00:20:25.518][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:20:25.522][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-12-20 00:20:25.525][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:20:25.528][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:20:25.531][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:20:25.535][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:25.537][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:20:25.540][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:20:25.546][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:25.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:25.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:25.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:25.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:25.570][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:25.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:25.575][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-12-20 00:20:25.582][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:25.584][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:25.597][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-12-20 00:20:26.031][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-12-20 00:20:26.444][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:26.449][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-12-20 00:20:26.458][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-12-20 00:20:26.465][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-12-20 00:20:26.468][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:20:26.473][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:20:26.476][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:20:26.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:26.482][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:26.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:26.498][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:26.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:26.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:26.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:26.509][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:26.512][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:26.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.517][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:26.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:26.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.531][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:26.533][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:26.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.538][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.541][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:26.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:26.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.551][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:26.553][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:26.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.558][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.561][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:26.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:26.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.571][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:26.573][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:26.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.578][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.581][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:26.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:26.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.590][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:26.593][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:26.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.597][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.600][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:26.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:26.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.610][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:26.613][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:26.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.617][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.620][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:26.623][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:26.625][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.627][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.630][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:26.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:26.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.640][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:26.643][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:26.646][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.648][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:26.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:26.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.663][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:26.665][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:26.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.669][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.672][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:26.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:26.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.683][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:26.686][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:26.688][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.690][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.693][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:26.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:26.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.717][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:26.720][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:26.722][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.725][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.728][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:26.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:26.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:26.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:26.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.749][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:26.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:26.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:26.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:26.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:26.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:26.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:26.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:26.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:26.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:26.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:26.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:26.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:26.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:26.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:26.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:26.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:26.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:26.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:26.835][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-12-20 00:20:26.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:26.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:26.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:26.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:26.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:26.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:26.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:26.911][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:26.920][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:20:26.923][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-12-20 00:20:26.927][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:20:26.930][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-12-20 00:20:26.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:26.940][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:26.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:26.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:26.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:26.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:26.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:26.968][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:26.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:26.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:26.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:26.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:26.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:26.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:27.193][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:27.195][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:27.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:27.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:27.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:27.213][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:27.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:27.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.229][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:27.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:27.269][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:27.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:27.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:27.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:27.288][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:27.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:27.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:27.340][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:27.342][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:27.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:27.357][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:27.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:27.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:27.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:27.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:27.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:27.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:27.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:27.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:27.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:27.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:27.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:27.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.467][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:27.479][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:27.482][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:27.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:27.499][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:27.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:27.504][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:27.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:27.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.522][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:27.546][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:27.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:27.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:27.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:27.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:27.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:27.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:27.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:27.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:27.612][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:27.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:27.626][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:27.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:27.631][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:27.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:27.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.654][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:27.663][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:27.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:27.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:27.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:27.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:27.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:27.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:27.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:27.728][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:27.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:27.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:27.748][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:27.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:27.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:27.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:27.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:27.793][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:27.797][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:27.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:27.815][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:27.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:27.820][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:27.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:27.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:27.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:27.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:27.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:27.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:27.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:27.881][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:27.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:27.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:27.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:27.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:27.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:27.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:27.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:27.943][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:27.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:27.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:27.973][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:27.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:27.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:27.984][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:27.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:27.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:28.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:28.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:28.006][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:28.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:28.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:28.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:28.051][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:28.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:28.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:28.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:28.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:28.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:28.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:28.127][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:28.130][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:28.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:28.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:28.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:28.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:28.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:28.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.173][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:28.196][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:28.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:28.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:28.213][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:28.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:28.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:28.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:28.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:28.253][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:28.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:28.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:28.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:28.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:28.272][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:28.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:28.277][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:28.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:28.308][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:28.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:28.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:28.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:28.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:28.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:28.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.350][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:28.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:28.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:28.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:28.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:28.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:28.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:28.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:28.384][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:28.453][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:28.462][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:20:28.465][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-12-20 00:20:28.468][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:20:28.471][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-12-20 00:20:28.478][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:28.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:28.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:28.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:28.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:28.499][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:28.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:28.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.522][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:28.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:28.532][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:28.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:28.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:28.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:28.550][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:28.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:28.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.593][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:28.603][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:28.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:28.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:28.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:28.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:28.623][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:28.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:28.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:28.675][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:28.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:28.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:28.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:28.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:28.694][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:28.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:28.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.717][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:28.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:28.748][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:28.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:28.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:28.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:28.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:28.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:28.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:28.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:28.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:28.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:28.810][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:28.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:28.815][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:28.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:28.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:28.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:28.849][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:28.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:28.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:28.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:28.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:28.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:28.873][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:28.900][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:28.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:28.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:28.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:28.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:28.919][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:28.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:28.924][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:28.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:28.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:28.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:28.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:28.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:28.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:28.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:28.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:28.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:28.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:28.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:29.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:29.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:29.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:29.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:29.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:29.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:29.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:29.032][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:29.059][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:29.061][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:29.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:29.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:29.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:29.078][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:29.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:29.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:29.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:29.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:29.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:29.133][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:29.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:29.137][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:29.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:29.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:29.169][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:29.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:29.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:29.184][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:29.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:29.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:29.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:29.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:29.218][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:29.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:29.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:29.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:29.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:29.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:29.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:29.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:29.268][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:29.270][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:29.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:29.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:29.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:29.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:29.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:29.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:29.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:29.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:29.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:29.333][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:29.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:29.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:29.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:29.342][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.352][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.362][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:29.378][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:29.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:29.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:29.394][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:29.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:29.398][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:29.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:29.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:29.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:29.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:29.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:29.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:29.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:29.472][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:29.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:29.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:29.520][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:29.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:29.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:29.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:29.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:29.542][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:29.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:29.548][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:29.583][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:29.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:29.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:29.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:29.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:29.603][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:29.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:29.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:29.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.677][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-12-20 00:20:29.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-12-20 00:20:29.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-12-20 00:20:29.736][biodb::testThat]
biodb.INFO [2024-12-20 00:20:29.738][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-12-20 00:20:29.740][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:20:29.743][biodb::testThat]
biodb.TRACE[2024-12-20 00:20:29.749][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-20 00:20:29.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-20 00:20:29.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.761][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:29.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:29.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:29.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:29.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:29.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:29.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:29.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:29.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:29.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:29.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:29.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:29.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:29.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:29.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:29.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:29.845][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:29.853][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:20:29.857][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-12-20 00:20:29.860][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:20:29.863][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-12-20 00:20:29.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:29.871][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:29.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:29.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:29.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:29.893][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:29.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:29.898][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:29.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:29.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:29.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:29.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:29.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:29.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:29.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:29.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:29.973][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:29.987][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:20:29.991][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-12-20 00:20:29.993][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:20:29.995][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-12-20 00:20:29.999][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:30.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:30.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:30.013][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:30.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:30.017][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:30.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:30.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:30.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:30.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.031][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:30.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:30.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:30.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:30.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:30.050][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:30.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:30.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:30.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:30.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:30.069][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:30.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:30.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:30.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:30.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:30.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:30.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:30.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:30.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:30.103][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-12-20 00:20:30.106][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:30.108][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:30.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:30.122][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:30.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:30.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:30.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:30.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.148][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:30.151][private$selectFields]
biodb.TRACE[2024-12-20 00:20:30.153][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 00:20:30.155][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 00:20:30.157][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:30.159][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.162][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.166][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.168][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.171][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.173][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.176][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.181][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:30.184][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:30.187][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.190][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.195][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.197][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 00:20:30.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.256][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-12-20 00:20:30.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:30.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:30.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:30.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:30.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:30.278][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:30.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:30.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.302][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:30.305][private$selectFields]
biodb.TRACE[2024-12-20 00:20:30.307][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 00:20:30.309][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 00:20:30.312][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:30.314][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.317][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.321][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.323][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.326][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.328][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.330][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.333][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:30.335][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:30.338][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.340][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.343][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.345][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.347][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 00:20:30.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.379][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-12-20 00:20:30.382][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:30.384][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:30.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:30.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:30.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:30.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:30.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:30.407][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.429][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:30.431][private$selectFields]
biodb.TRACE[2024-12-20 00:20:30.433][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 00:20:30.436][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 00:20:30.438][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:30.440][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.443][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.445][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.447][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.450][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.453][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.458][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.461][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:30.464][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:30.467][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.470][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.475][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.477][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 00:20:30.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.500][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:30.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.512][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-12-20 00:20:30.515][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-12-20 00:20:30.517][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-12-20 00:20:30.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:30.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:30.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.552][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:30.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:30.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:30.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:30.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:30.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:30.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:30.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:30.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:30.731][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:30.733][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:30.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:30.748][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:30.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:30.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:30.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:30.761][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:30.769][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:30.771][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:30.777][private$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[2024-12-20 00:20:31.195][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[2024-12-20 00:20:31.602][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:31.615][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-12-20 00:20:31.631][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-12-20 00:20:31.638][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[2024-12-20 00:20:31.647][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:31.649][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:31.654][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-12-20 00:20:32.069][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-12-20 00:20:32.496][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:32.500][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-12-20 00:20:32.509][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-12-20 00:20:32.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:32.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:32.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:32.532][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:32.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:32.536][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:32.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:32.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:32.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:32.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:32.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:32.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:32.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:32.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:32.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:32.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:32.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:32.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:32.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:32.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:32.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:32.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:32.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:32.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:32.588][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:32.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:32.592][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:32.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:32.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:32.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:32.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:32.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:32.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:32.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:32.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:32.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:32.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:32.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:32.620][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:32.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:32.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:32.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:32.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:32.638][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:32.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:32.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:32.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:32.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:32.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:32.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:32.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:32.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:32.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:32.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:32.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:32.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:32.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:32.734][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-12-20 00:20:32.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:32.803][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:32.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:32.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:32.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:32.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:32.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:32.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:32.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:32.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:32.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:32.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:32.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:32.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:32.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:32.844][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:32.846][private$selectFields]
biodb.TRACE[2024-12-20 00:20:32.848][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 00:20:32.851][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 00:20:32.853][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:32.855][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:32.858][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:32.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:32.863][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:32.865][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:32.868][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:32.871][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:32.874][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:32.876][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:32.879][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:32.881][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:32.884][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:32.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:32.889][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:32.891][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 00:20:32.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:32.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:32.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:32.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:32.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:32.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:32.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:32.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:32.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:32.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:32.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:32.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:32.924][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-12-20 00:20:32.926][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:32.928][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:32.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:32.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:32.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:32.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:32.948][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[2024-12-20 00:20:32.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:32.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:32.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:32.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:32.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.067][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:33.069][private$selectFields]
biodb.TRACE[2024-12-20 00:20:33.072][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 00:20:33.074][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 00:20:33.076][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:33.079][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.081][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.084][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.086][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.088][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.091][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.096][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.098][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:33.126][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:33.128][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.131][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.135][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.137][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 00:20:33.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.168][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-12-20 00:20:33.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:33.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:33.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:33.186][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:33.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:33.190][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:33.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:33.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.214][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:33.216][private$selectFields]
biodb.TRACE[2024-12-20 00:20:33.218][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 00:20:33.220][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 00:20:33.223][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:33.225][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.227][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.250][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.257][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.259][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.262][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.272][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.279][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:33.282][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:33.284][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.286][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.290][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.293][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 00:20:33.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.323][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-12-20 00:20:33.325][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-12-20 00:20:33.327][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-12-20 00:20:33.347][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-12-20 00:20:33.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-12-20 00:20:33.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-12-20 00:20:33.363][biodb::testThat]
biodb.INFO [2024-12-20 00:20:33.365][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-12-20 00:20:33.367][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:20:33.369][biodb::testThat]
biodb.TRACE[2024-12-20 00:20:33.375][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-20 00:20:33.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-20 00:20:33.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.384][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.393][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:33.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:33.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:33.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:33.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:33.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:33.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:33.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:33.452][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:33.460][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:20:33.463][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-12-20 00:20:33.466][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:20:33.469][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-12-20 00:20:33.474][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:33.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:33.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:33.489][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:33.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:33.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:33.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:33.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:33.526][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:33.534][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:20:33.537][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-12-20 00:20:33.540][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:20:33.543][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-12-20 00:20:33.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:33.550][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:33.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:33.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:33.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:33.568][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:33.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:33.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.582][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.591][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:33.600][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:33.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:33.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:33.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:33.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:33.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:33.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:33.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:33.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:33.649][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-12-20 00:20:33.653][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:33.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:33.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:33.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:33.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:33.672][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:33.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:33.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.696][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:33.699][private$selectFields]
biodb.TRACE[2024-12-20 00:20:33.701][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 00:20:33.703][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 00:20:33.705][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:33.708][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.710][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.712][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.715][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.717][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.720][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.722][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.725][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.727][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:33.729][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:33.731][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.733][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.735][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.737][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.740][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 00:20:33.742][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.760][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.769][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-12-20 00:20:33.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:33.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:33.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:33.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:33.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:33.793][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:33.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:33.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.816][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:33.818][private$selectFields]
biodb.TRACE[2024-12-20 00:20:33.820][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 00:20:33.823][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 00:20:33.825][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:33.828][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.830][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.834][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.836][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.839][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.843][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.845][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:33.847][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:33.849][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.852][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.856][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.858][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 00:20:33.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.888][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-12-20 00:20:33.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:33.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:33.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:33.905][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:33.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:33.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:33.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:33.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.933][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:33.935][private$selectFields]
biodb.TRACE[2024-12-20 00:20:33.937][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 00:20:33.939][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 00:20:33.941][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:33.943][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.946][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.950][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.953][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.955][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.960][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.962][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:33.964][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:33.967][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.969][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.973][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.975][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 00:20:33.978][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:33.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:33.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:33.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.007][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-12-20 00:20:34.010][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-12-20 00:20:34.012][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-12-20 00:20:34.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.053][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.063][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:34.087][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:34.089][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:34.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:34.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:34.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:34.108][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:34.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:34.116][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:34.123][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:20:34.126][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-12-20 00:20:34.129][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:20:34.132][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-12-20 00:20:34.138][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:34.146][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:20:34.149][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-12-20 00:20:34.151][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:20:34.154][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-12-20 00:20:34.159][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:34.161][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:34.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:34.173][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:34.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:34.177][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:34.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:34.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:34.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:34.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:34.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:34.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:34.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:34.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:34.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:34.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.243][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:34.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:34.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:34.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:34.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:34.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:34.280][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:34.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:34.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:34.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:34.312][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-12-20 00:20:34.315][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:34.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:34.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:34.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:34.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:34.335][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:34.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:34.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.349][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.358][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:34.360][private$selectFields]
biodb.TRACE[2024-12-20 00:20:34.363][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 00:20:34.365][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 00:20:34.367][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:34.369][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.371][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.373][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.375][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.378][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.380][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.384][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.387][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:34.389][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:34.391][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.393][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.395][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.397][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.399][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 00:20:34.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.431][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-12-20 00:20:34.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:34.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:34.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:34.448][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:34.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:34.452][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:34.455][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.TRACE[2024-12-20 00:20:34.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.476][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:34.478][private$selectFields]
biodb.TRACE[2024-12-20 00:20:34.480][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 00:20:34.482][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 00:20:34.484][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:34.486][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.489][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.493][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.495][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.498][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.502][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.505][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:34.507][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:34.509][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.512][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.517][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.519][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 00:20:34.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.540][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.551][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-12-20 00:20:34.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:34.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:34.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:34.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:34.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:34.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:34.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:34.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.598][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:34.600][private$selectFields]
biodb.TRACE[2024-12-20 00:20:34.602][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 00:20:34.604][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 00:20:34.607][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:34.609][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.612][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.616][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.619][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.622][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.627][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.629][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:34.632][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:34.634][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.637][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.641][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.643][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 00:20:34.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:34.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.675][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-12-20 00:20:34.677][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-12-20 00:20:34.680][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-12-20 00:20:34.701][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-12-20 00:20:34.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-12-20 00:20:34.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-12-20 00:20:34.719][biodb::testThat]
biodb.INFO [2024-12-20 00:20:34.721][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-12-20 00:20:34.724][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:20:34.726][biodb::testThat]
biodb.TRACE[2024-12-20 00:20:34.733][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-20 00:20:34.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-20 00:20:34.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:34.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:34.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.754][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:34.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:34.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:34.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:34.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:34.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:34.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:34.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:34.793][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:34.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:34.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:34.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:34.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:34.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:34.819][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:34.827][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:20:34.830][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-12-20 00:20:34.833][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:20:34.836][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-12-20 00:20:34.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:34.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:34.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:34.858][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:34.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:34.863][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:34.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:34.868][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:34.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:34.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:34.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:34.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:34.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:34.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:34.907][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:34.915][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:20:34.918][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-12-20 00:20:34.922][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:20:34.925][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-12-20 00:20:34.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:34.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:34.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:34.945][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:34.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:34.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:34.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:34.955][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:34.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:34.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.964][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:34.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:34.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:34.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:34.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:34.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:34.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:34.984][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:34.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:34.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:35.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:35.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:35.005][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:35.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:35.010][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:35.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:35.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:35.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:35.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.029][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:35.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:35.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:35.038][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-12-20 00:20:35.042][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:35.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:35.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:35.057][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:35.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:35.061][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:35.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:35.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.094][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:35.096][private$selectFields]
biodb.TRACE[2024-12-20 00:20:35.099][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 00:20:35.113][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 00:20:35.117][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:35.119][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.121][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.129][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.135][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.137][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.141][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.144][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:35.146][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:35.149][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.151][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.155][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.157][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 00:20:35.159][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.189][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-12-20 00:20:35.196][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:35.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:35.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:35.214][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:35.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:35.220][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:35.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:35.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.267][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:35.270][private$selectFields]
biodb.TRACE[2024-12-20 00:20:35.272][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 00:20:35.275][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 00:20:35.277][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:35.280][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.283][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.287][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.290][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.292][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.297][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.300][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:35.302][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:35.305][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.307][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.312][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.314][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 00:20:35.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.335][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.345][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-12-20 00:20:35.348][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:35.350][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:35.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:35.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:35.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:35.368][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:35.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:35.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.393][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:35.395][private$selectFields]
biodb.TRACE[2024-12-20 00:20:35.398][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 00:20:35.400][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 00:20:35.402][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:35.405][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.407][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.412][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.414][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.417][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.421][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.424][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:35.427][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:35.429][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.432][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.434][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.437][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.439][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 00:20:35.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:35.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.507][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-12-20 00:20:35.517][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-12-20 00:20:35.519][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-12-20 00:20:35.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:35.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:35.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.632][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:35.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:35.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:35.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:35.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.654][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:35.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:35.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:35.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:35.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:35.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:35.694][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:35.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:35.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:35.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:35.765][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:35.774][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:20:35.777][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-12-20 00:20:35.780][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:20:35.784][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-12-20 00:20:35.791][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:35.804][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:20:35.808][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-12-20 00:20:35.812][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:20:35.883][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-12-20 00:20:35.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:35.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:35.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:35.905][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:35.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:35.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:35.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:35.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:35.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:35.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:35.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:35.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:35.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:35.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:35.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:35.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:35.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:35.989][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:35.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:36.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:36.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:36.008][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:36.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:36.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:36.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:36.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:36.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:36.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:36.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:36.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:36.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:36.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:36.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:36.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:36.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:36.066][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:36.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:36.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:36.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:36.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:36.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:36.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:36.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:36.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:36.107][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-12-20 00:20:36.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:36.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:36.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:36.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:36.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:36.143][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:36.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:36.165][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.184][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:36.186][private$selectFields]
biodb.TRACE[2024-12-20 00:20:36.188][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 00:20:36.190][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 00:20:36.192][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:36.194][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.196][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.198][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.200][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.202][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.204][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.208][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.211][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:36.213][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:36.215][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.217][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.219][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.221][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.223][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 00:20:36.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.254][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-12-20 00:20:36.256][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:36.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:36.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:36.270][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:36.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:36.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:36.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:36.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.291][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.300][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:36.303][private$selectFields]
biodb.TRACE[2024-12-20 00:20:36.305][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 00:20:36.307][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 00:20:36.309][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:36.312][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.314][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.319][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.321][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.324][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.329][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.331][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:36.333][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:36.335][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.339][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.343][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.345][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 00:20:36.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.357][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.367][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.377][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-12-20 00:20:36.380][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:36.382][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:36.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:36.395][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:36.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:36.399][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:36.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:36.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.424][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:36.427][private$selectFields]
biodb.TRACE[2024-12-20 00:20:36.429][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 00:20:36.431][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 00:20:36.434][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:36.437][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.439][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.442][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.444][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.446][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.449][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.454][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.456][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:36.458][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 00:20:36.461][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.464][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.468][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.472][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 00:20:36.500][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:36.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:36.532][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-12-20 00:20:36.534][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-12-20 00:20:36.537][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-12-20 00:20:36.584][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-12-20 00:20:36.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-12-20 00:20:36.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:36.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-12-20 00:20:36.602][biodb::testThat]
biodb.INFO [2024-12-20 00:20:36.604][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-12-20 00:20:36.606][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:20:36.608][biodb::testThat]
biodb.DEBUG[2024-12-20 00:20:36.612][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-12-20 00:20:36.615][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:20:36.619][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-12-20 00:20:36.622][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:20:36.625][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:20:36.627][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:20:36.630][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:36.632][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:20:36.634][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:20:36.640][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:36.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:36.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:36.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:36.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:36.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:36.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:36.665][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-12-20 00:20:36.672][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:36.674][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:36.677][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-12-20 00:20:37.087][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-12-20 00:20:37.510][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:37.514][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-12-20 00:20:37.521][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-12-20 00:20:37.527][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-12-20 00:20:37.530][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:20:37.533][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:20:37.536][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:20:37.539][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:37.541][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:37.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:37.554][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:37.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:37.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:37.559][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.TRACE[2024-12-20 00:20:37.564][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:37.566][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:37.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.570][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:37.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:37.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:37.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:37.581][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:37.584][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:37.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.588][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:37.591][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:37.593][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:37.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.597][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:37.600][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:37.602][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:37.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.606][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:37.609][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:37.611][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:37.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.615][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:37.618][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:37.621][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:37.623][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.625][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:37.628][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:37.630][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:37.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.634][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:37.637][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:37.640][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:37.642][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.644][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:37.647][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:37.649][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:37.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.653][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:37.656][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:37.658][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:37.660][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.662][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:37.665][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:37.667][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:37.669][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.671][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:37.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:37.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:37.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:37.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:37.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:37.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:37.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:37.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:37.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:37.701][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:37.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:37.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:37.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:37.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:37.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:37.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:37.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:37.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:37.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:37.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:37.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:37.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:37.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:37.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:37.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:37.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:37.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:37.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:37.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:37.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:37.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:37.766][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-12-20 00:20:37.768][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-12-20 00:20:37.799][biodb::testThat]
biodb.INFO [2024-12-20 00:20:37.801][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-12-20 00:20:37.803][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:20:37.805][biodb::testThat]
biodb.DEBUG[2024-12-20 00:20:37.828][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-12-20 00:20:37.830][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-12-20 00:20:37.833][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-12-20 00:20:37.836][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-12-20 00:20:37.839][cch$loadFileContent] file.exist = [3]: "FALSE, TRUE, FALSE".
biodb.TRACE[2024-12-20 00:20:37.843][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml".
biodb.DEBUG[2024-12-20 00:20:37.845][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:20:37.847][conn$getEntryContent] 2 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:37.850][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:20:37.852][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:20:37.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:37.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:37.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:37.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:37.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:37.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:37.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:37.882][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-12-20 00:20:37.888][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:37.890][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:37.892][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-12-20 00:20:38.307][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-12-20 00:20:38.733][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:38.738][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-12-20 00:20:38.746][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-12-20 00:20:38.750][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:38.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:38.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:38.765][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:38.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:38.769][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:38.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:38.774][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-12-20 00:20:38.781][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:38.783][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:38.787][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-12-20 00:20:39.214][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-12-20 00:20:39.640][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:39.645][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-12-20 00:20:39.653][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-12-20 00:20:39.659][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-12-20 00:20:39.664][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:20:39.667][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-12-20 00:20:39.669][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-12-20 00:20:39.673][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:39.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:39.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:39.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:39.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:39.693][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:39.695][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.TRACE[2024-12-20 00:20:39.700][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:39.703][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:39.705][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:39.708][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:39.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:39.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:39.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:39.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:39.721][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:39.724][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:39.727][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:39.729][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:39.732][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:39.735][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:39.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:39.740][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:39.744][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:39.746][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:39.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:39.751][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:39.754][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:39.757][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:39.759][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:39.762][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:39.765][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:39.767][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:39.770][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:39.772][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:39.775][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:39.777][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:39.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:39.782][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:39.784][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:39.787][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:39.789][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:39.791][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:39.794][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:39.796][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:39.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:39.801][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:39.804][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:39.806][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:39.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:39.811][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:39.814][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:39.816][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:39.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:39.820][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:39.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:39.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:39.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:39.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:39.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:39.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:39.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:39.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:39.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:39.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:39.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:39.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:39.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:39.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:39.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:39.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:39.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:39.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:39.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:39.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:39.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:39.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:39.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:39.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:39.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:39.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:39.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:39.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:39.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:39.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:39.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:39.983][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:39.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:39.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:40.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:40.011][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:40.014][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:40.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.018][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:40.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:40.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.032][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:40.034][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:40.037][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.039][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.046][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:40.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:40.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.064][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:40.067][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:40.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.071][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.074][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:40.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:40.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.120][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:40.135][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:40.137][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.139][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.146][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:40.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:40.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.156][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:40.159][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:40.161][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.163][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.165][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:40.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:40.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.175][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:40.177][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:40.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.181][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.185][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:40.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:40.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.231][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:40.233][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:40.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.237][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.245][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:40.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:40.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.258][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:40.262][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:40.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.270][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.273][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:40.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:40.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.283][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:40.285][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:40.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.289][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.294][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:40.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:40.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.333][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:40.337][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:40.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.345][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.348][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:40.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:40.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.367][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:40.370][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:40.372][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.375][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.378][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:40.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:40.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:40.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:40.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:40.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:40.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:40.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:40.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:40.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:40.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:40.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:40.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:40.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:40.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:40.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:40.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:40.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:40.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:40.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:40.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:40.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:40.508][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:40.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 00:20:40.524][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:40.526][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:40.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.532][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:40.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:40.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.557][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:40.560][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:40.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.568][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.571][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:20:40.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:20:40.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.581][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:40.584][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:40.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.588][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.591][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:20:40.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:20:40.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.611][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:40.614][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:40.634][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.636][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.639][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:20:40.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:20:40.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.648][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:40.650][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:40.652][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.654][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.656][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:20:40.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:20:40.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.665][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:40.668][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:40.670][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.672][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.675][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:40.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:20:40.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.685][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:40.688][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:40.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.692][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.695][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:20:40.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:20:40.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.704][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:40.706][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:40.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.709][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.712][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:40.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:40.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.720][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:40.723][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:40.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.727][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.730][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:40.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:40.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.738][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:40.740][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:40.742][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.744][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.747][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:20:40.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:20:40.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.756][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:40.759][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:40.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.763][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.766][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:20:40.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:20:40.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.775][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:40.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:40.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.785][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:40.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:40.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:40.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:40.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:20:40.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:20:40.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:40.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:40.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:40.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:40.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:40.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:40.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:40.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:40.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:40.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:40.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:40.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:40.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:40.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:40.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:40.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:40.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:40.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:40.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:40.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:40.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:40.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:40.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:40.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:20:40.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:20:40.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:40.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:20:40.919][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-12-20 00:20:40.922][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-12-20 00:20:40.924][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-12-20 00:20:40.955][biodb::testThat]
biodb.INFO [2024-12-20 00:20:40.957][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-12-20 00:20:40.959][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:20:40.961][biodb::testThat]
biodb.INFO [2024-12-20 00:20:41.031][biodb::testThat]
biodb.INFO [2024-12-20 00:20:41.035][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-12-20 00:20:41.038][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:20:41.040][biodb::testThat]
biodb.INFO [2024-12-20 00:20:41.062][biodb::testThat]
biodb.INFO [2024-12-20 00:20:41.065][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-12-20 00:20:41.067][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:20:41.069][biodb::testThat]
biodb.DEBUG[2024-12-20 00:20:41.075][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[2024-12-20 00:20:41.084][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:41.086][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:41.091][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-12-20 00:20:41.646][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-12-20 00:20:42.178][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2024-12-20 00:20:42.182][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-12-20 00:20:42.186][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-12-20 00:20:42.196][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-12-20 00:20:42.224][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:20:42.227][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:20:42.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:42.231][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:20:42.233][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:42.236][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:20:42.238][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:20:42.240][ef$get] fields variable is a list.
biodb.INFO [2024-12-20 00:20:42.243][biodb::testThat]
biodb.INFO [2024-12-20 00:20:42.246][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-12-20 00:20:42.248][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:20:42.250][biodb::testThat]
biodb.ERROR[2024-12-20 00:20:42.282][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-12-20 00:20:42.318][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-12-20 00:20:42.350][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-12-20 00:20:42.353][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-12-20 00:20:42.355][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-12-20 00:20:42.357][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-12-20 00:20:42.360][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:42.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:42.363][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:42.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:42.368][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:42.370][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.INFO [2024-12-20 00:20:42.395][biodb::testContext]
biodb.INFO [2024-12-20 00:20:42.398][biodb::testContext] ********************************************************************************
biodb.INFO [2024-12-20 00:20:42.400][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-12-20 00:20:42.403][biodb::testContext] ********************************************************************************
biodb.INFO [2024-12-20 00:20:42.405][biodb::testContext]
biodb.INFO [2024-12-20 00:20:42.410][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-12-20 00:20:42.413][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-12-20 00:20:42.421][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 00:20:42.424][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-12-20 00:20:42.426][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-12-20 00:20:42.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:42.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:42.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:42.436][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-12-20 00:20:42.485][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-12-20 00:20:42.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:42.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:42.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:42.494][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-12-20 00:20:42.496][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-12-20 00:20:42.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:42.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:42.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:42.504][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-12-20 00:20:42.507][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-12-20 00:20:42.509][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-12-20 00:20:42.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:42.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:42.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:42.533][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-12-20 00:20:42.536][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-12-20 00:20:42.538][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-12-20 00:20:42.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:42.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:42.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:42.547][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-12-20 00:20:42.549][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-12-20 00:20:42.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:42.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:42.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:42.558][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-12-20 00:20:42.560][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-12-20 00:20:42.562][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-12-20 00:20:42.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:42.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:42.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:42.570][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-12-20 00:20:42.573][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-12-20 00:20:42.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:42.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:42.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:42.581][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-12-20 00:20:42.583][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-12-20 00:20:42.586][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-12-20 00:20:42.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:42.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:42.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:42.594][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-12-20 00:20:42.596][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-12-20 00:20:42.599][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-12-20 00:20:42.601][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-12-20 00:20:42.603][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-12-20 00:20:42.605][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-12-20 00:20:42.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:42.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:42.612][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[2024-12-20 00:20:42.614][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-12-20 00:20:42.617][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-12-20 00:20:42.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:42.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:42.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:42.625][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-12-20 00:20:42.627][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-12-20 00:20:42.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:42.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:42.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:42.636][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-12-20 00:20:42.638][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-12-20 00:20:42.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:42.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:42.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:42.647][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-12-20 00:20:42.650][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-12-20 00:20:42.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:42.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:42.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:42.659][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-12-20 00:20:42.661][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-12-20 00:20:42.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:42.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:42.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:42.671][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-12-20 00:20:42.673][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-12-20 00:20:42.694][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-12-20 00:20:42.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:42.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:42.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:42.702][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-12-20 00:20:42.705][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-12-20 00:20:42.707][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-12-20 00:20:42.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:42.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:42.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:42.717][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-12-20 00:20:42.721][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:42.723][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-12-20 00:20:42.726][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:42.728][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 00:20:42.730][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:42.733][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 00:20:42.735][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:42.737][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 00:20:42.739][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-12-20 00:20:42.742][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 00:20:42.744][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:42.746][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-12-20 00:20:42.749][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 00:20:42.751][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:42.754][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:42.756][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 00:20:42.756][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 00:20:42.756][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 00:20:42.756][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-12-20 00:20:42.756][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-12-20 00:20:42.759][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 00:20:42.761][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:42.763][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:42.766][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 00:20:42.768][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:42.770][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:42.773][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 00:20:42.775][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:42.777][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 00:20:42.780][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 00:20:42.782][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:42.785][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:42.788][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-12-20 00:20:42.792][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:42.795][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-12-20 00:20:42.797][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:42.800][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 00:20:42.802][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:42.805][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 00:20:42.808][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:42.810][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 00:20:42.813][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-12-20 00:20:42.815][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 00:20:42.817][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:42.820][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-12-20 00:20:42.822][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 00:20:42.825][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:42.827][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:42.831][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 00:20:42.831][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 00:20:42.831][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 00:20:42.831][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-12-20 00:20:42.831][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-12-20 00:20:42.834][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 00:20:42.836][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:42.838][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:42.841][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 00:20:42.844][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:42.846][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:42.848][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 00:20:42.851][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:42.853][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 00:20:42.855][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 00:20:42.857][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:42.860][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:42.863][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-12-20 00:20:42.868][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:42.870][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-12-20 00:20:42.872][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:42.875][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 00:20:42.877][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:42.879][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 00:20:42.882][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:42.884][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 00:20:42.886][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-12-20 00:20:42.889][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 00:20:42.891][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:42.893][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-12-20 00:20:42.896][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 00:20:42.898][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:42.901][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:42.903][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:42.905][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 00:20:42.908][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:42.910][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:42.912][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 00:20:42.914][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:42.916][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:42.919][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 00:20:42.921][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:42.924][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 00:20:42.926][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 00:20:42.929][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:42.931][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:42.934][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-12-20 00:20:42.938][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:42.940][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-12-20 00:20:42.943][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:42.946][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 00:20:42.949][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:42.951][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 00:20:42.954][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:42.956][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 00:20:42.959][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-12-20 00:20:42.961][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 00:20:42.964][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:42.967][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-12-20 00:20:42.969][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 00:20:42.972][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:42.974][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:42.977][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:42.979][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 00:20:42.982][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:42.984][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:42.986][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 00:20:42.988][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:42.990][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:42.993][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 00:20:42.995][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:42.997][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 00:20:42.999][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 00:20:43.001][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:43.004][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:43.007][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 00:20:43.009][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.021][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[2024-12-20 00:20:43.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.031][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[2024-12-20 00:20:43.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.042][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[2024-12-20 00:20:43.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.131][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[2024-12-20 00:20:43.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.200][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-12-20 00:20:43.203][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-12-20 00:20:43.207][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-12-20 00:20:43.211][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-12-20 00:20:43.215][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-12-20 00:20:43.218][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-12-20 00:20:43.222][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-12-20 00:20:43.225][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-12-20 00:20:43.229][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-12-20 00:20:43.233][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-12-20 00:20:43.236][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-12-20 00:20:43.240][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-12-20 00:20:43.243][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-12-20 00:20:43.247][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-12-20 00:20:43.251][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-12-20 00:20:43.255][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-12-20 00:20:43.259][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-12-20 00:20:43.263][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-12-20 00:20:43.266][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-12-20 00:20:43.270][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-12-20 00:20:43.274][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-12-20 00:20:43.278][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-12-20 00:20:43.282][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-12-20 00:20:43.285][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-12-20 00:20:43.289][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-12-20 00:20:43.292][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-12-20 00:20:43.296][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-12-20 00:20:43.299][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-12-20 00:20:43.303][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-12-20 00:20:43.306][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-12-20 00:20:43.310][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-12-20 00:20:43.313][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-12-20 00:20:43.316][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-12-20 00:20:43.319][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-12-20 00:20:43.323][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-12-20 00:20:43.326][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-12-20 00:20:43.329][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-12-20 00:20:43.333][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-12-20 00:20:43.337][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-12-20 00:20:43.340][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-12-20 00:20:43.343][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-12-20 00:20:43.355][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-12-20 00:20:43.359][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-12-20 00:20:43.363][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-12-20 00:20:43.366][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-12-20 00:20:43.369][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-12-20 00:20:43.373][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-12-20 00:20:43.376][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-12-20 00:20:43.379][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-12-20 00:20:43.382][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-12-20 00:20:43.386][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-12-20 00:20:43.389][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-12-20 00:20:43.392][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-12-20 00:20:43.396][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-12-20 00:20:43.399][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-12-20 00:20:43.402][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-12-20 00:20:43.406][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-12-20 00:20:43.409][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-12-20 00:20:43.412][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-12-20 00:20:43.415][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-12-20 00:20:43.419][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-12-20 00:20:43.422][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-12-20 00:20:43.425][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-12-20 00:20:43.428][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-12-20 00:20:43.432][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-12-20 00:20:43.435][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-12-20 00:20:43.438][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-12-20 00:20:43.441][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-12-20 00:20:43.444][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-12-20 00:20:43.448][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-12-20 00:20:43.451][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-12-20 00:20:43.454][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-12-20 00:20:43.457][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-12-20 00:20:43.460][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-12-20 00:20:43.463][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-12-20 00:20:43.466][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-12-20 00:20:43.470][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-12-20 00:20:43.473][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-12-20 00:20:43.476][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-12-20 00:20:43.479][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-12-20 00:20:43.482][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-12-20 00:20:43.485][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-12-20 00:20:43.488][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-12-20 00:20:43.491][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-12-20 00:20:43.495][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-12-20 00:20:43.497][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 00:20:43.499][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.503][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:43.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:43.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:43.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:43.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.533][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[2024-12-20 00:20:43.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:43.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:43.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:43.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:43.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:43.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:43.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.575][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[2024-12-20 00:20:43.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:43.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:43.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:43.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:43.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:43.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:43.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:43.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:43.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.631][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[2024-12-20 00:20:43.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:43.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:43.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:43.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:43.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:43.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:43.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:43.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:43.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:43.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:43.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:43.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:43.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:43.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:43.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.731][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[2024-12-20 00:20:43.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:43.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:43.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:43.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:43.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:43.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:43.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:43.748][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-12-20 00:20:43.751][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-12-20 00:20:43.756][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:43.758][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-12-20 00:20:43.761][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:43.763][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 00:20:43.766][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:43.768][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 00:20:43.770][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:43.773][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-12-20 00:20:43.775][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-12-20 00:20:43.777][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 00:20:43.780][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:43.782][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-12-20 00:20:43.784][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 00:20:43.787][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-12-20 00:20:43.787][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-12-20 00:20:43.787][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-12-20 00:20:43.787][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-12-20 00:20:43.787][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-12-20 00:20:43.787][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-12-20 00:20:43.787][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-12-20 00:20:43.787][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-12-20 00:20:43.787][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-12-20 00:20:43.787][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-12-20 00:20:43.787][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-12-20 00:20:43.789][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:43.792][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 00:20:43.792][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 00:20:43.792][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 00:20:43.794][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-12-20 00:20:43.796][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:43.798][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:43.800][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 00:20:43.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:43.805][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:43.807][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 00:20:43.809][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:43.809][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-12-20 00:20:43.811][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 00:20:43.814][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 00:20:43.816][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:43.818][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-12-20 00:20:43.818][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-12-20 00:20:43.821][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-12-20 00:20:43.826][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-12-20 00:20:43.830][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-12-20 00:20:43.834][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-12-20 00:20:43.843][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-12-20 00:20:43.847][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-12-20 00:20:43.858][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-12-20 00:20:43.861][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-12-20 00:20:43.864][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-12-20 00:20:43.868][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-12-20 00:20:43.871][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-12-20 00:20:43.874][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-12-20 00:20:43.877][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-12-20 00:20:43.880][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-12-20 00:20:43.883][biodb::testThat]
biodb.INFO [2024-12-20 00:20:43.888][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-12-20 00:20:43.890][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:20:43.893][biodb::testThat]
biodb.DEBUG[2024-12-20 00:20:43.901][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-12-20 00:20:43.911][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:43.913][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:43.916][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-12-20 00:20:44.421][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-12-20 00:20:44.954][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:44.958][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-12-20 00:20:44.968][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-12-20 00:20:45.042][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:45.050][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:45.054][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:45.058][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-12-20 00:20:45.498][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[2024-12-20 00:20:45.914][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:45.918][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-12-20 00:20:45.927][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-12-20 00:20:45.932][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:45.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:45.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:45.947][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:45.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:45.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:45.953][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[2024-12-20 00:20:45.957][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[2024-12-20 00:20:45.965][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:45.967][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:45.971][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-12-20 00:20:46.387][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-12-20 00:20:46.797][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:46.801][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-12-20 00:20:46.811][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-12-20 00:20:46.816][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:46.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:46.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:46.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:46.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:46.837][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:46.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:46.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:46.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:46.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:46.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:46.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:46.927][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:46.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:46.940][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:46.948][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:20:46.952][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-12-20 00:20:46.955][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:20:46.958][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-12-20 00:20:46.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:46.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:46.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:46.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:46.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:46.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:46.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:46.987][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:46.994][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:20:46.997][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-12-20 00:20:47.000][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:20:47.003][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-12-20 00:20:47.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:47.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:47.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:47.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:47.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:47.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:47.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:47.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:47.032][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:47.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:47.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:47.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:47.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:47.052][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[2024-12-20 00:20:47.061][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:47.070][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:20:47.073][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-12-20 00:20:47.076][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:20:47.079][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-12-20 00:20:47.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:47.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:47.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:47.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:47.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:47.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:47.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:47.107][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:47.115][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:20:47.118][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-12-20 00:20:47.121][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:20:47.124][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-12-20 00:20:47.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:47.130][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:47.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:47.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:47.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:47.147][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:47.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:47.153][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:47.161][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:47.163][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:47.168][private$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[2024-12-20 00:20:47.596][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[2024-12-20 00:20:48.010][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:48.014][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-12-20 00:20:48.023][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-12-20 00:20:48.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:48.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:48.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:48.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:48.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:48.047][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:48.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-12-20 00:20:48.064][biodb::testThat]
biodb.INFO [2024-12-20 00:20:48.066][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-12-20 00:20:48.069][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:20:48.071][biodb::testThat]
biodb.DEBUG[2024-12-20 00:20:48.077][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:48.086][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:48.088][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:48.094][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-12-20 00:20:48.590][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-12-20 00:20:49.002][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2024-12-20 00:20:49.005][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-12-20 00:20:49.009][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-12-20 00:20:49.019][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-12-20 00:20:49.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:49.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:49.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:49.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:49.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:49.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:49.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:49.056][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[2024-12-20 00:20:49.064][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:49.066][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:49.070][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-12-20 00:20:49.488][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-12-20 00:20:49.894][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:49.898][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-12-20 00:20:49.908][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-12-20 00:20:49.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:49.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:49.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:49.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:49.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:49.931][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:49.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-12-20 00:20:49.945][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-12-20 00:20:49.948][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-12-20 00:20:49.951][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-12-20 00:20:49.953][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-12-20 00:20:49.955][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:49.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:49.959][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:49.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:49.963][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:49.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-12-20 00:20:49.974][biodb::testContext]
biodb.INFO [2024-12-20 00:20:49.976][biodb::testContext] ********************************************************************************
biodb.INFO [2024-12-20 00:20:49.979][biodb::testContext] Test context - Test web services
biodb.INFO [2024-12-20 00:20:49.982][biodb::testContext] ********************************************************************************
biodb.INFO [2024-12-20 00:20:49.984][biodb::testContext]
biodb.INFO [2024-12-20 00:20:49.989][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-12-20 00:20:49.993][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-12-20 00:20:50.001][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 00:20:50.004][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-12-20 00:20:50.006][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-12-20 00:20:50.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:50.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:50.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:50.015][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-12-20 00:20:50.064][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-12-20 00:20:50.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:50.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:50.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:50.072][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-12-20 00:20:50.074][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-12-20 00:20:50.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:50.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:50.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:50.082][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-12-20 00:20:50.085][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-12-20 00:20:50.087][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-12-20 00:20:50.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:50.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:50.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:50.096][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-12-20 00:20:50.098][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-12-20 00:20:50.101][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-12-20 00:20:50.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:50.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:50.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:50.109][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-12-20 00:20:50.111][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-12-20 00:20:50.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:50.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:50.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:50.119][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-12-20 00:20:50.122][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-12-20 00:20:50.124][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-12-20 00:20:50.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:50.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:50.130][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[2024-12-20 00:20:50.133][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-12-20 00:20:50.135][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-12-20 00:20:50.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:50.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:50.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:50.143][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-12-20 00:20:50.146][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-12-20 00:20:50.148][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-12-20 00:20:50.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:50.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:50.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:50.156][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-12-20 00:20:50.158][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-12-20 00:20:50.161][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-12-20 00:20:50.163][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-12-20 00:20:50.165][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-12-20 00:20:50.167][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-12-20 00:20:50.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:50.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:50.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:50.176][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-12-20 00:20:50.179][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-12-20 00:20:50.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:50.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:50.185][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[2024-12-20 00:20:50.187][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-12-20 00:20:50.189][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-12-20 00:20:50.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:50.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:50.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:50.198][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-12-20 00:20:50.200][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-12-20 00:20:50.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:50.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:50.206][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[2024-12-20 00:20:50.209][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-12-20 00:20:50.219][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-12-20 00:20:50.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:50.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:50.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:50.242][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-12-20 00:20:50.245][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-12-20 00:20:50.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:50.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:50.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:50.253][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-12-20 00:20:50.255][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-12-20 00:20:50.293][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-12-20 00:20:50.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:50.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:50.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:50.302][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-12-20 00:20:50.355][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-12-20 00:20:50.358][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-12-20 00:20:50.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:50.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:50.373][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[2024-12-20 00:20:50.376][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-12-20 00:20:50.380][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:50.385][self$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[2024-12-20 00:20:50.387][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:50.390][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 00:20:50.392][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:50.400][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 00:20:50.402][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:50.404][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 00:20:50.407][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-12-20 00:20:50.409][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 00:20:50.416][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:50.419][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-12-20 00:20:50.422][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 00:20:50.424][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:50.427][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:50.440][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 00:20:50.440][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 00:20:50.440][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 00:20:50.440][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-12-20 00:20:50.440][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-12-20 00:20:50.443][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 00:20:50.445][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:50.447][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:50.450][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 00:20:50.460][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:50.462][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:50.464][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 00:20:50.466][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:50.482][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 00:20:50.485][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 00:20:50.487][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:50.490][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:50.503][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-12-20 00:20:50.508][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:50.510][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-12-20 00:20:50.512][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:50.530][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 00:20:50.532][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:50.535][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 00:20:50.538][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:50.551][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 00:20:50.553][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-12-20 00:20:50.556][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 00:20:50.558][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:50.570][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-12-20 00:20:50.572][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 00:20:50.575][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:50.577][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:50.590][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 00:20:50.590][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 00:20:50.590][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 00:20:50.590][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-12-20 00:20:50.590][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-12-20 00:20:50.594][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 00:20:50.597][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:50.599][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:50.611][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 00:20:50.613][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:50.615][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:50.617][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 00:20:50.619][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:50.631][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 00:20:50.633][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 00:20:50.635][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:50.638][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:50.641][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-12-20 00:20:50.645][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:50.647][self$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[2024-12-20 00:20:50.659][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:50.661][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 00:20:50.664][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:50.666][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 00:20:50.682][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:50.685][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 00:20:50.687][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-12-20 00:20:50.690][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 00:20:50.701][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:50.704][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-12-20 00:20:50.706][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 00:20:50.708][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:50.720][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:50.722][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:50.725][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 00:20:50.727][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:50.729][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:50.742][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 00:20:50.745][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:50.747][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:50.749][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 00:20:50.761][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:50.764][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 00:20:50.766][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 00:20:50.768][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:50.776][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:50.780][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-12-20 00:20:50.785][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:50.798][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-12-20 00:20:50.803][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:50.806][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 00:20:50.812][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:50.815][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 00:20:50.818][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:50.838][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 00:20:50.841][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-12-20 00:20:50.844][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 00:20:50.847][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:50.865][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-12-20 00:20:50.868][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 00:20:50.871][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:50.873][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:50.900][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:50.908][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 00:20:50.911][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:50.940][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:50.943][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 00:20:50.949][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:50.953][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:51.000][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 00:20:51.002][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:51.004][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 00:20:51.006][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 00:20:51.008][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:51.022][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:51.026][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 00:20:51.028][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:51.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:51.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:51.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:51.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:51.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:51.054][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.DEBUG[2024-12-20 00:20:51.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:51.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:51.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:51.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:51.071][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[2024-12-20 00:20:51.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:51.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:51.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:51.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:51.097][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[2024-12-20 00:20:51.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:51.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:51.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:51.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:51.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:51.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:51.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:51.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:51.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:51.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:51.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:51.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:51.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:51.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:51.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:51.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:51.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:51.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:51.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:51.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:51.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:51.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:51.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:51.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:51.208][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[2024-12-20 00:20:51.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:51.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:51.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:51.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:51.229][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[2024-12-20 00:20:51.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:51.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:51.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:51.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:51.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:51.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:51.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:51.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:51.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:51.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:51.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:51.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:51.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:51.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:51.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:51.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:51.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:51.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:51.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:51.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:51.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:51.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:51.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:51.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:51.319][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[2024-12-20 00:20:51.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:51.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:51.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:51.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:51.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:51.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:51.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:51.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:51.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:51.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:51.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:51.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:51.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:51.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:51.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:51.418][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-12-20 00:20:51.421][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-12-20 00:20:51.435][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-12-20 00:20:51.438][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-12-20 00:20:51.441][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-12-20 00:20:51.453][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-12-20 00:20:51.457][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-12-20 00:20:51.460][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-12-20 00:20:51.473][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-12-20 00:20:51.476][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-12-20 00:20:51.479][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-12-20 00:20:51.495][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-12-20 00:20:51.499][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-12-20 00:20:51.503][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-12-20 00:20:51.520][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-12-20 00:20:51.524][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-12-20 00:20:51.537][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-12-20 00:20:51.541][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-12-20 00:20:51.544][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-12-20 00:20:51.557][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-12-20 00:20:51.560][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-12-20 00:20:51.564][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-12-20 00:20:51.571][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-12-20 00:20:51.575][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-12-20 00:20:51.578][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-12-20 00:20:51.592][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-12-20 00:20:51.596][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-12-20 00:20:51.600][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-12-20 00:20:51.616][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-12-20 00:20:51.619][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-12-20 00:20:51.646][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-12-20 00:20:51.650][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-12-20 00:20:51.655][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-12-20 00:20:51.668][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-12-20 00:20:51.671][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-12-20 00:20:51.675][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-12-20 00:20:51.685][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-12-20 00:20:51.689][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-12-20 00:20:51.692][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-12-20 00:20:51.705][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-12-20 00:20:51.708][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-12-20 00:20:51.712][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-12-20 00:20:51.727][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-12-20 00:20:51.730][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-12-20 00:20:51.743][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-12-20 00:20:51.747][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-12-20 00:20:51.750][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-12-20 00:20:51.768][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-12-20 00:20:51.773][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-12-20 00:20:51.778][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-12-20 00:20:51.781][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-12-20 00:20:51.784][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-12-20 00:20:51.788][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-12-20 00:20:51.800][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-12-20 00:20:51.803][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-12-20 00:20:51.806][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-12-20 00:20:51.823][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-12-20 00:20:51.827][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-12-20 00:20:51.840][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-12-20 00:20:51.844][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-12-20 00:20:51.847][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-12-20 00:20:51.860][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-12-20 00:20:51.864][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-12-20 00:20:51.867][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-12-20 00:20:51.882][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-12-20 00:20:51.885][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-12-20 00:20:51.889][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-12-20 00:20:51.905][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-12-20 00:20:51.914][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-12-20 00:20:51.917][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-12-20 00:20:51.938][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-12-20 00:20:51.943][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-12-20 00:20:51.946][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-12-20 00:20:51.961][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-12-20 00:20:51.964][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-12-20 00:20:51.987][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-12-20 00:20:52.002][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-12-20 00:20:52.006][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-12-20 00:20:52.009][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-12-20 00:20:52.025][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-12-20 00:20:52.028][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-12-20 00:20:52.032][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-12-20 00:20:52.047][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-12-20 00:20:52.050][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-12-20 00:20:52.054][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-12-20 00:20:52.067][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 00:20:52.069][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:52.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:52.073][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:52.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:52.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:52.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:52.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:52.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:52.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:52.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:52.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:52.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:52.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:52.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:52.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:52.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:52.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:52.130][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[2024-12-20 00:20:52.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:52.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:52.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:52.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:52.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:52.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:52.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:52.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:52.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:52.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:52.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:52.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:52.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:52.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:52.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:52.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:52.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:52.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:52.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:52.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:52.229][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[2024-12-20 00:20:52.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:52.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:52.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:52.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:52.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:52.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:52.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:52.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:52.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:52.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:52.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:52.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:52.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:52.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:52.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:52.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:52.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:52.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:52.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:52.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:52.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:52.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:52.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:52.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:52.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:52.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:52.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:52.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:52.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:52.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:52.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:52.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:52.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:52.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:52.387][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[2024-12-20 00:20:52.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:52.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:52.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:52.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:52.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:52.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:52.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:52.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:52.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:52.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:52.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:52.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:52.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:52.438][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[2024-12-20 00:20:52.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:52.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:52.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:52.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:52.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:52.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:52.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:52.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:52.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:52.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:52.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:52.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:52.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:52.499][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[2024-12-20 00:20:52.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:52.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:52.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:52.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:52.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:52.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:52.542][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[2024-12-20 00:20:52.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:52.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:52.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:52.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:52.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:52.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:52.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:52.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:52.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:52.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:52.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:52.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:52.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:52.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:52.608][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-12-20 00:20:52.622][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-12-20 00:20:52.627][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:52.630][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-12-20 00:20:52.658][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:52.663][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 00:20:52.668][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:52.697][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 00:20:52.699][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:52.701][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-12-20 00:20:52.703][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-12-20 00:20:52.715][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 00:20:52.719][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:52.722][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-12-20 00:20:52.724][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 00:20:52.738][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-12-20 00:20:52.738][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-12-20 00:20:52.738][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-12-20 00:20:52.738][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-12-20 00:20:52.738][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-12-20 00:20:52.738][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-12-20 00:20:52.738][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-12-20 00:20:52.738][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-12-20 00:20:52.738][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-12-20 00:20:52.738][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-12-20 00:20:52.738][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-12-20 00:20:52.741][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:52.744][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 00:20:52.744][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 00:20:52.744][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 00:20:52.756][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-12-20 00:20:52.759][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:52.761][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:52.765][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 00:20:52.822][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:52.824][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:52.827][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 00:20:52.829][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:52.829][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-12-20 00:20:52.831][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 00:20:52.833][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 00:20:52.836][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:52.838][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-12-20 00:20:52.838][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-12-20 00:20:52.841][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-12-20 00:20:52.877][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-12-20 00:20:52.881][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-12-20 00:20:52.892][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-12-20 00:20:52.895][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-12-20 00:20:52.899][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-12-20 00:20:52.916][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-12-20 00:20:52.919][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-12-20 00:20:52.930][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-12-20 00:20:52.934][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-12-20 00:20:52.937][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-12-20 00:20:52.951][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-12-20 00:20:52.954][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-12-20 00:20:52.957][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-12-20 00:20:52.960][biodb::testThat]
biodb.INFO [2024-12-20 00:20:52.971][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-12-20 00:20:52.974][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:20:52.976][biodb::testThat]
biodb.DEBUG[2024-12-20 00:20:52.992][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-12-20 00:20:53.009][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:53.011][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:53.014][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-12-20 00:20:53.431][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-12-20 00:20:53.935][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:53.939][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-12-20 00:20:53.948][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-12-20 00:20:54.013][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[2024-12-20 00:20:54.021][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:54.023][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:54.027][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-12-20 00:20:54.435][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-12-20 00:20:54.836][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:20:54.841][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-12-20 00:20:54.850][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-12-20 00:20:54.869][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-12-20 00:20:54.871][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-12-20 00:20:54.874][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-12-20 00:20:54.876][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-12-20 00:20:54.878][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:54.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:54.881][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:54.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:54.885][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:54.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-12-20 00:20:54.895][biodb::testContext]
biodb.INFO [2024-12-20 00:20:54.897][biodb::testContext] ********************************************************************************
biodb.INFO [2024-12-20 00:20:54.899][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-12-20 00:20:54.902][biodb::testContext] ********************************************************************************
biodb.INFO [2024-12-20 00:20:54.904][biodb::testContext]
biodb.INFO [2024-12-20 00:20:54.908][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-12-20 00:20:54.912][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-12-20 00:20:54.919][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 00:20:54.922][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-12-20 00:20:54.924][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-12-20 00:20:54.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:54.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:54.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:54.932][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-12-20 00:20:54.979][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-12-20 00:20:54.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:54.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:54.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:54.988][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-12-20 00:20:54.991][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-12-20 00:20:54.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:55.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:55.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:55.010][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-12-20 00:20:55.012][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-12-20 00:20:55.023][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-12-20 00:20:55.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:55.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:55.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:55.040][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-12-20 00:20:55.042][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-12-20 00:20:55.045][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-12-20 00:20:55.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:55.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:55.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:55.064][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-12-20 00:20:55.071][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-12-20 00:20:55.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:55.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:55.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:55.086][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-12-20 00:20:55.088][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-12-20 00:20:55.100][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-12-20 00:20:55.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:55.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:55.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:55.156][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-12-20 00:20:55.159][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-12-20 00:20:55.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:55.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:55.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:55.178][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-12-20 00:20:55.180][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-12-20 00:20:55.182][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-12-20 00:20:55.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:55.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:55.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:55.201][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-12-20 00:20:55.203][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-12-20 00:20:55.216][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-12-20 00:20:55.218][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-12-20 00:20:55.221][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-12-20 00:20:55.223][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-12-20 00:20:55.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:55.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:55.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:55.240][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-12-20 00:20:55.243][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-12-20 00:20:55.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:55.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:55.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:55.276][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-12-20 00:20:55.290][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-12-20 00:20:55.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:55.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:55.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:55.308][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-12-20 00:20:55.311][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-12-20 00:20:55.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:55.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:55.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:55.328][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-12-20 00:20:55.331][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-12-20 00:20:55.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:55.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:55.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:55.348][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-12-20 00:20:55.350][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-12-20 00:20:55.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:55.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:55.356][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[2024-12-20 00:20:55.370][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-12-20 00:20:55.373][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-12-20 00:20:55.396][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-12-20 00:20:55.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:55.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:55.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:55.404][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-12-20 00:20:55.416][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-12-20 00:20:55.418][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-12-20 00:20:55.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:55.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:55.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:55.433][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-12-20 00:20:55.437][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:55.440][self$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[2024-12-20 00:20:55.446][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:55.448][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 00:20:55.450][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:55.453][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 00:20:55.464][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:55.466][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 00:20:55.468][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-12-20 00:20:55.470][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 00:20:55.473][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:55.483][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-12-20 00:20:55.485][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 00:20:55.488][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:55.491][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:55.514][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 00:20:55.514][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 00:20:55.514][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 00:20:55.514][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-12-20 00:20:55.514][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-12-20 00:20:55.517][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 00:20:55.519][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:55.521][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:55.525][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 00:20:55.529][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:55.542][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:55.545][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 00:20:55.554][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:55.556][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 00:20:55.558][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 00:20:55.561][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:55.570][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:55.573][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-12-20 00:20:55.577][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:55.589][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-12-20 00:20:55.592][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:55.594][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 00:20:55.596][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:55.605][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 00:20:55.607][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:55.610][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 00:20:55.612][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-12-20 00:20:55.614][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 00:20:55.656][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:55.658][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-12-20 00:20:55.661][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 00:20:55.663][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:55.675][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:55.677][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 00:20:55.677][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 00:20:55.677][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 00:20:55.677][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-12-20 00:20:55.677][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-12-20 00:20:55.679][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 00:20:55.682][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:55.694][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:55.696][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 00:20:55.698][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:55.700][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:55.710][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 00:20:55.713][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:55.715][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 00:20:55.717][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 00:20:55.719][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:55.732][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:55.734][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-12-20 00:20:55.739][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:55.751][self$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[2024-12-20 00:20:55.753][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:55.756][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 00:20:55.759][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:55.788][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 00:20:55.791][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:55.793][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 00:20:55.795][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-12-20 00:20:55.806][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 00:20:55.808][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:55.811][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-12-20 00:20:55.813][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 00:20:55.825][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:55.828][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:55.830][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:55.832][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 00:20:55.835][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:55.846][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:55.848][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 00:20:55.850][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:55.852][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:55.865][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 00:20:55.868][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:55.870][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 00:20:55.872][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 00:20:55.874][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:55.889][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:55.891][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-12-20 00:20:55.896][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:55.910][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-12-20 00:20:55.913][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:55.915][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 00:20:55.917][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:55.929][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 00:20:55.931][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:55.933][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 00:20:55.935][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-12-20 00:20:55.945][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 00:20:55.948][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:55.950][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-12-20 00:20:55.952][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 00:20:55.954][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:55.967][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:55.969][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:55.971][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 00:20:55.973][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:55.985][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:55.988][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 00:20:55.990][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:55.992][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:55.994][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 00:20:56.011][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:56.014][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 00:20:56.016][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 00:20:56.018][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:56.031][self$setPropertyValue]
biodb.DEBUG[2024-12-20 00:20:56.034][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 00:20:56.036][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:56.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:56.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:56.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:56.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:56.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:56.054][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.DEBUG[2024-12-20 00:20:56.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:56.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:56.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:56.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:56.076][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[2024-12-20 00:20:56.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:56.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:56.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:56.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:56.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:56.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:56.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:56.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:56.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:56.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:56.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:56.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:56.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:56.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:56.153][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[2024-12-20 00:20:56.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:56.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:56.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:56.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:56.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:56.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:56.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:56.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:56.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:56.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:56.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:56.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:56.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:56.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:56.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:56.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:56.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:56.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:56.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:56.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:56.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:56.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:56.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:56.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:56.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:56.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:56.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:56.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:56.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:56.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:56.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:56.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:56.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:56.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:56.310][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[2024-12-20 00:20:56.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:56.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:56.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:56.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:56.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:56.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:56.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:56.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:56.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:56.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:56.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:56.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:56.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:56.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:56.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:56.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:56.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:56.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:56.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:56.381][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[2024-12-20 00:20:56.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:56.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:56.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:56.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:56.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:56.416][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-12-20 00:20:56.419][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-12-20 00:20:56.423][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-12-20 00:20:56.445][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-12-20 00:20:56.448][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-12-20 00:20:56.452][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-12-20 00:20:56.464][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-12-20 00:20:56.468][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-12-20 00:20:56.472][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-12-20 00:20:56.483][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-12-20 00:20:56.486][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-12-20 00:20:56.501][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-12-20 00:20:56.507][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-12-20 00:20:56.518][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-12-20 00:20:56.541][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-12-20 00:20:56.544][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-12-20 00:20:56.548][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-12-20 00:20:56.563][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-12-20 00:20:56.567][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-12-20 00:20:56.579][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-12-20 00:20:56.583][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-12-20 00:20:56.586][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-12-20 00:20:56.600][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-12-20 00:20:56.604][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-12-20 00:20:56.607][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-12-20 00:20:56.624][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-12-20 00:20:56.628][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-12-20 00:20:56.633][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-12-20 00:20:56.658][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-12-20 00:20:56.662][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-12-20 00:20:56.675][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-12-20 00:20:56.679][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-12-20 00:20:56.682][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-12-20 00:20:56.695][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-12-20 00:20:56.699][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-12-20 00:20:56.702][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-12-20 00:20:56.714][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-12-20 00:20:56.717][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-12-20 00:20:56.721][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-12-20 00:20:56.734][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-12-20 00:20:56.737][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-12-20 00:20:56.741][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-12-20 00:20:56.756][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-12-20 00:20:56.760][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-12-20 00:20:56.774][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-12-20 00:20:56.778][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-12-20 00:20:56.782][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-12-20 00:20:56.794][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-12-20 00:20:56.816][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-12-20 00:20:56.819][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-12-20 00:20:56.823][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-12-20 00:20:56.835][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-12-20 00:20:56.838][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-12-20 00:20:56.852][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-12-20 00:20:56.855][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-12-20 00:20:56.858][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-12-20 00:20:56.882][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-12-20 00:20:56.891][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-12-20 00:20:56.894][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-12-20 00:20:56.909][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-12-20 00:20:56.912][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-12-20 00:20:56.924][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-12-20 00:20:56.928][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-12-20 00:20:56.932][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-12-20 00:20:56.943][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-12-20 00:20:56.947][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-12-20 00:20:56.961][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-12-20 00:20:56.965][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-12-20 00:20:56.969][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-12-20 00:20:56.983][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-12-20 00:20:56.987][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-12-20 00:20:57.000][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-12-20 00:20:57.004][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-12-20 00:20:57.007][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-12-20 00:20:57.031][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-12-20 00:20:57.034][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-12-20 00:20:57.038][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-12-20 00:20:57.048][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-12-20 00:20:57.051][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-12-20 00:20:57.055][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-12-20 00:20:57.071][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-12-20 00:20:57.074][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-12-20 00:20:57.077][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-12-20 00:20:57.089][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-12-20 00:20:57.093][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-12-20 00:20:57.095][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 00:20:57.107][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:57.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:57.112][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:57.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:57.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:57.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:57.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:57.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:57.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:57.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:57.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:57.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:57.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:57.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:57.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:57.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:57.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:57.191][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.DEBUG[2024-12-20 00:20:57.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:57.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:57.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:57.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:57.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:57.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:57.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:57.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:57.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:57.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:57.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:57.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:57.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:57.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:57.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:57.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:57.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:57.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:57.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:57.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:57.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:57.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:57.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:57.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:57.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:57.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:57.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:57.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:57.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:57.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:57.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:57.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:57.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:57.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:57.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:57.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:57.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:57.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:57.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:57.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:57.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:57.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:57.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:57.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:57.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:57.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:57.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:57.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:57.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:57.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:57.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:57.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:57.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:57.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:57.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:57.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:57.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:57.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:57.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:57.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:57.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:57.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:57.548][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[2024-12-20 00:20:57.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:57.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:57.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:57.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:57.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:57.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:57.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:57.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:57.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:57.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:57.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:57.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:57.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:57.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:57.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:57.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:57.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:57.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:57.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:57.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:57.644][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[2024-12-20 00:20:57.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:57.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:57.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:57.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:57.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:57.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:57.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:57.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:57.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:57.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:57.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:57.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:57.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:57.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:57.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 00:20:57.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:57.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:57.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:57.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:57.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:57.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:57.730][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-12-20 00:20:57.742][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-12-20 00:20:57.746][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:57.762][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-12-20 00:20:57.766][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:57.768][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 00:20:57.770][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:57.773][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 00:20:57.787][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:57.789][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-12-20 00:20:57.791][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-12-20 00:20:57.793][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 00:20:57.804][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:57.806][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-12-20 00:20:57.809][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 00:20:57.812][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-12-20 00:20:57.812][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-12-20 00:20:57.812][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-12-20 00:20:57.812][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-12-20 00:20:57.812][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-12-20 00:20:57.812][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-12-20 00:20:57.812][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-12-20 00:20:57.812][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-12-20 00:20:57.812][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-12-20 00:20:57.812][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-12-20 00:20:57.812][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-12-20 00:20:57.824][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-12-20 00:20:57.826][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 00:20:57.826][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 00:20:57.826][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 00:20:57.828][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-12-20 00:20:57.840][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:57.843][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:57.845][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 00:20:57.847][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 00:20:57.849][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 00:20:57.862][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 00:20:57.864][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:57.864][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-12-20 00:20:57.867][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 00:20:57.869][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 00:20:57.871][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-12-20 00:20:57.874][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-12-20 00:20:57.874][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-12-20 00:20:57.877][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-12-20 00:20:57.913][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-12-20 00:20:57.916][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-12-20 00:20:57.919][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-12-20 00:20:57.932][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-12-20 00:20:57.936][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-12-20 00:20:57.952][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-12-20 00:20:57.954][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-12-20 00:20:57.957][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-12-20 00:20:57.969][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-12-20 00:20:57.972][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-12-20 00:20:57.975][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-12-20 00:20:57.988][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-12-20 00:20:57.991][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-12-20 00:20:57.994][biodb::testThat]
biodb.INFO [2024-12-20 00:20:57.997][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-12-20 00:20:57.999][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 00:20:58.001][biodb::testThat]
biodb.DEBUG[2024-12-20 00:20:58.008][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-12-20 00:20:58.040][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:20:58.058][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-12-20 00:20:58.061][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:20:58.064][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-12-20 00:20:58.254][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-12-20 00:20:58.275][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 00:20:58.278][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-12-20 00:20:58.284][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 00:20:58.300][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-12-20 00:20:58.323][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-12-20 00:20:58.326][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 00:20:58.342][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-12-20 00:20:58.347][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 00:20:58.354][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 00:20:58.371][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 00:20:58.374][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 00:20:58.377][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 00:20:58.380][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 00:20:58.396][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:20:58.398][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:20:58.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:20:58.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:20:58.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:20:58.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:20:58.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 00:20:58.441][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-12-20 00:20:58.458][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 00:20:58.460][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 00:20:58.476][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-12-20 00:21:00.758][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-12-20 00:21:01.443][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 00:21:01.447][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-12-20 00:21:01.456][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-12-20 00:21:01.462][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-12-20 00:21:01.467][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 00:21:01.470][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 00:21:01.472][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 00:21:01.476][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 00:21:01.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:21:01.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:21:01.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:21:01.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:21:01.496][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:21:01.498][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[2024-12-20 00:21:01.507][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:21:01.510][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:21:01.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.528][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:21:01.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:21:01.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.540][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:21:01.542][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:21:01.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.547][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.550][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 00:21:01.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 00:21:01.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.559][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:21:01.562][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:21:01.564][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.566][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.569][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 00:21:01.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 00:21:01.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.587][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 00:21:01.594][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 00:21:01.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.598][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.602][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 00:21:01.611][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 00:21:01.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.616][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.619][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:21:01.630][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:21:01.633][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.635][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.640][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:21:01.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 00:21:01.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.669][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:21:01.671][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:21:01.674][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.676][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.690][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 00:21:01.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 00:21:01.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.712][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:21:01.715][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:21:01.717][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.719][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:21:01.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 00:21:01.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.752][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:21:01.755][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:21:01.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.760][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.786][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 00:21:01.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 00:21:01.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.806][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:21:01.809][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:21:01.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.813][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.826][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 00:21:01.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 00:21:01.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.843][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:21:01.845][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:21:01.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.850][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.862][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 00:21:01.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 00:21:01.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.889][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:21:01.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:21:01.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:21:01.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:21:01.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:21:01.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:21:01.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 00:21:01.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 00:21:01.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:21:01.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:21:01.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:01.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:01.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:21:01.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:21:01.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:02.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:02.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:21:02.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:21:02.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:02.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:02.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:21:02.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:21:02.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:02.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:02.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:21:02.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:21:02.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:02.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 00:21:02.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 00:21:02.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 00:21:02.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 00:21:02.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 00:21:02.098][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-12-20 00:21:02.118][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-12-20 00:21:02.121][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-12-20 00:21:02.124][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-12-20 00:21:02.146][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-12-20 00:21:02.148][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 00:21:02.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 00:21:02.153][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 00:21:02.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 00:21:02.170][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 00:21:02.172][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 385 ]
>
> proc.time()
user system elapsed
40.378 1.999 87.355
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 4.747 | 1.247 | 7.006 | |
| ChebiEntry | 0.765 | 0.018 | 0.789 | |