Pierrick Roger
| Snapshot Date: 2025-03-19 13:40 -0400 (Wed, 19 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: devel |
| git_last_commit: 686a27c |
| git_last_commit_date: 2024-10-29 11:04:36 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-20 11:43 -0400 (Thu, 20 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4777 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4458 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 204/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.13.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbChebi |
| Version: 1.13.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.13.0.tar.gz |
| StartedAt: 2025-03-19 19:43:46 -0400 (Wed, 19 Mar 2025) |
| EndedAt: 2025-03-19 19:45:55 -0400 (Wed, 19 Mar 2025) |
| EllapsedTime: 128.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘biodbChebi’ ... ** this is package ‘biodbChebi’ version ‘1.13.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2025-03-19 19:44:43.190][biodb::testContext]
biodb.INFO [2025-03-19 19:44:43.194][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-19 19:44:43.195][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-03-19 19:44:43.196][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-19 19:44:43.197][biodb::testContext]
biodb.INFO [2025-03-19 19:44:43.204][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-19 19:44:43.207][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-19 19:44:43.215][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 19:44:43.216][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-19 19:44:43.217][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-19 19:44:43.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.222][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-19 19:44:43.244][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-19 19:44:43.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.250][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-19 19:44:43.251][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-19 19:44:43.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.256][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-19 19:44:43.257][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-19 19:44:43.258][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-19 19:44:43.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.262][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-19 19:44:43.264][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-19 19:44:43.265][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-19 19:44:43.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.270][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-19 19:44:43.272][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-19 19:44:43.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.275][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[2025-03-19 19:44:43.276][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-19 19:44:43.278][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-19 19:44:43.279][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-19 19:44:43.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.284][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-19 19:44:43.285][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-19 19:44:43.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.289][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-19 19:44:43.290][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-19 19:44:43.291][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-19 19:44:43.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.296][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-19 19:44:43.297][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-19 19:44:43.298][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-19 19:44:43.300][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-19 19:44:43.301][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-19 19:44:43.302][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-19 19:44:43.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.307][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-19 19:44:43.309][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-19 19:44:43.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.314][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-19 19:44:43.315][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-19 19:44:43.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.320][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-19 19:44:43.321][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-19 19:44:43.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.325][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-19 19:44:43.327][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-19 19:44:43.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.332][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-19 19:44:43.333][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-19 19:44:43.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.338][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-19 19:44:43.339][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-19 19:44:43.369][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-19 19:44:43.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.374][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-19 19:44:43.375][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-19 19:44:43.377][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-19 19:44:43.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.383][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-19 19:44:43.425][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 19:44:43.454][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-19 19:44:43.456][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 19:44:43.458][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 19:44:43.459][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 19:44:43.461][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 19:44:43.462][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 19:44:43.464][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 19:44:43.465][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-19 19:44:43.466][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 19:44:43.468][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 19:44:43.469][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-19 19:44:43.470][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 19:44:43.472][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:44:43.473][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 19:44:43.474][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 19:44:43.474][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 19:44:43.474][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 19:44:43.474][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-19 19:44:43.474][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-19 19:44:43.476][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 19:44:43.477][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:44:43.478][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:44:43.479][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 19:44:43.480][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:44:43.481][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:44:43.483][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 19:44:43.484][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:44:43.486][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 19:44:43.487][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 19:44:43.488][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 19:44:43.489][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:44:43.491][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-19 19:44:43.493][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 19:44:43.494][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-19 19:44:43.495][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 19:44:43.497][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 19:44:43.498][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 19:44:43.499][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 19:44:43.500][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 19:44:43.502][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 19:44:43.503][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-19 19:44:43.504][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 19:44:43.505][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 19:44:43.506][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-19 19:44:43.507][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 19:44:43.508][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:44:43.509][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 19:44:43.510][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 19:44:43.510][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 19:44:43.510][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 19:44:43.510][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-19 19:44:43.510][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-19 19:44:43.512][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 19:44:43.513][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:44:43.513][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:44:43.514][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 19:44:43.516][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:44:43.517][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:44:43.518][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 19:44:43.519][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:44:43.520][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 19:44:43.521][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 19:44:43.522][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 19:44:43.523][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:44:43.524][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-19 19:44:43.527][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-19 19:44:43.528][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-19 19:44:43.529][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 19:44:43.530][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 19:44:43.532][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 19:44:43.533][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 19:44:43.534][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 19:44:43.535][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 19:44:43.536][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-19 19:44:43.538][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 19:44:43.539][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-19 19:44:43.540][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-19 19:44:43.541][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 19:44:43.543][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:44:43.544][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 19:44:43.546][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:44:43.547][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 19:44:43.548][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:44:43.549][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:44:43.550][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 19:44:43.551][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:44:43.552][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:44:43.553][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 19:44:43.555][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:44:43.556][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 19:44:43.557][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 19:44:43.558][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 19:44:43.560][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:44:43.561][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-19 19:44:43.563][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-19 19:44:43.565][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-19 19:44:43.566][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 19:44:43.567][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 19:44:43.568][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 19:44:43.569][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 19:44:43.570][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 19:44:43.572][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 19:44:43.573][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-19 19:44:43.574][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 19:44:43.575][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-19 19:44:43.576][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-19 19:44:43.577][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 19:44:43.578][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:44:43.579][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 19:44:43.580][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:44:43.581][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 19:44:43.583][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:44:43.584][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:44:43.585][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 19:44:43.587][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:44:43.587][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:44:43.588][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 19:44:43.590][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:44:43.591][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 19:44:43.592][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 19:44:43.593][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 19:44:43.595][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:44:43.599][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 19:44:43.600][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.645][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[2025-03-19 19:44:43.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.674][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[2025-03-19 19:44:43.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.702][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-19 19:44:43.708][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-19 19:44:43.711][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-19 19:44:43.713][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-19 19:44:43.715][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-19 19:44:43.717][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-19 19:44:43.719][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-19 19:44:43.721][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-19 19:44:43.723][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-19 19:44:43.725][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-19 19:44:43.727][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-19 19:44:43.729][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-19 19:44:43.730][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-19 19:44:43.732][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-19 19:44:43.734][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-19 19:44:43.736][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-19 19:44:43.738][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-19 19:44:43.739][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-19 19:44:43.741][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-19 19:44:43.743][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-19 19:44:43.744][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-19 19:44:43.746][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-19 19:44:43.748][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-19 19:44:43.750][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-19 19:44:43.752][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-19 19:44:43.754][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-19 19:44:43.755][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-19 19:44:43.757][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-19 19:44:43.759][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-19 19:44:43.760][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-19 19:44:43.762][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-19 19:44:43.763][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-19 19:44:43.765][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-19 19:44:43.767][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-19 19:44:43.769][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-19 19:44:43.770][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-19 19:44:43.771][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-19 19:44:43.773][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-19 19:44:43.774][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-19 19:44:43.776][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-19 19:44:43.778][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-19 19:44:43.780][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-19 19:44:43.782][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-19 19:44:43.783][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-19 19:44:43.786][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-19 19:44:43.788][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-19 19:44:43.790][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-19 19:44:43.791][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-19 19:44:43.793][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-19 19:44:43.795][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-19 19:44:43.797][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-19 19:44:43.799][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-19 19:44:43.800][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-19 19:44:43.802][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-19 19:44:43.804][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-19 19:44:43.805][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-19 19:44:43.807][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-19 19:44:43.808][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-19 19:44:43.810][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-19 19:44:43.811][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-19 19:44:43.813][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-19 19:44:43.814][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-19 19:44:43.816][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-19 19:44:43.818][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-19 19:44:43.819][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-19 19:44:43.821][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-19 19:44:43.823][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-19 19:44:43.824][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-19 19:44:43.826][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-19 19:44:43.828][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-19 19:44:43.830][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-19 19:44:43.832][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-19 19:44:43.833][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-19 19:44:43.835][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-19 19:44:43.837][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-19 19:44:43.839][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-19 19:44:43.841][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-19 19:44:43.842][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-19 19:44:43.844][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-19 19:44:43.846][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-19 19:44:43.848][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-19 19:44:43.850][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-19 19:44:43.852][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-19 19:44:43.860][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-19 19:44:43.862][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-19 19:44:43.865][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 19:44:43.866][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.868][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:43.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:43.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:43.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:43.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:43.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:43.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:43.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:43.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:43.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:43.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:43.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:43.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:43.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:43.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:43.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:43.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:43.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:43.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:43.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:43.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:43.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:43.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:43.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:43.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:43.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:43.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:43.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:43.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:43.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:43.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:43.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:43.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:43.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:43.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:44:43.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:43.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:43.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:43.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:43.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:44.000][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[2025-03-19 19:44:44.002][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-19 19:44:44.014][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-19 19:44:44.016][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 19:44:44.017][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-19 19:44:44.018][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 19:44:44.019][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 19:44:44.021][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 19:44:44.022][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 19:44:44.023][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-19 19:44:44.025][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-19 19:44:44.026][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-19 19:44:44.027][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 19:44:44.029][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 19:44:44.030][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-19 19:44:44.031][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 19:44:44.032][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-19 19:44:44.032][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-19 19:44:44.032][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-19 19:44:44.032][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-19 19:44:44.032][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-19 19:44:44.032][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-19 19:44:44.032][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-19 19:44:44.032][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-19 19:44:44.032][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-19 19:44:44.032][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-19 19:44:44.032][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-19 19:44:44.033][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-19 19:44:44.034][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 19:44:44.034][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 19:44:44.034][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 19:44:44.035][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-19 19:44:44.037][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:44:44.038][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:44:44.039][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 19:44:44.040][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:44:44.040][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:44:44.042][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 19:44:44.043][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:44:44.043][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-19 19:44:44.044][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 19:44:44.045][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 19:44:44.046][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-19 19:44:44.047][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-19 19:44:44.047][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-19 19:44:44.054][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-19 19:44:44.056][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-19 19:44:44.058][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-19 19:44:44.059][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-19 19:44:44.061][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-19 19:44:44.063][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-19 19:44:44.094][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-19 19:44:44.096][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-19 19:44:44.101][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-19 19:44:44.106][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-19 19:44:44.147][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-19 19:44:44.148][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-19 19:44:44.150][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-19 19:44:44.151][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-19 19:44:44.160][biodb::testThat]
biodb.INFO [2025-03-19 19:44:44.161][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-03-19 19:44:44.163][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:44:44.164][biodb::testThat]
biodb.TRACE[2025-03-19 19:44:44.169][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-03-19 19:44:44.171][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:44:44.175][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:44:44.183][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:44.184][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:44.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:44.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:44.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:44.204][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:44.206][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.TRACE[2025-03-19 19:44:44.215][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:44.217][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:44.217][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.218][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:44.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:44.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.239][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:44.240][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:44.241][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.242][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.268][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:44.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:44.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.273][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:44.274][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:44.275][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.275][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.277][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:44.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:44.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.281][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:44.282][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:44.283][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.284][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.285][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:44.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:44.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.290][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:44.291][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:44.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.293][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.295][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:44.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:44.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.299][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:44.300][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:44.301][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.302][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.304][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:44.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:44.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.308][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:44:44.309][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:44.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.311][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.312][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:44:44.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:44.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.317][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:44.318][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:44.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.320][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:44.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:44.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.325][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:44.326][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:44.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.328][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.339][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:44.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:44.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.343][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:44.344][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:44.345][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.346][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.348][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:44.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:44.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.352][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:44.353][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:44.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.355][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.356][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:44.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:44.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.367][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:44.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:44.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:44.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:44.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:44.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:44.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:44.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:44.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:44.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:44.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:44.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:44.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:44.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:44.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:44.443][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-03-19 19:44:44.446][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:44.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:44.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.450][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:44.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:44.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.484][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:44.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:44.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:44.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:44.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:44.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:44.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.503][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:44.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:44.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.506][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-19 19:44:44.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-19 19:44:44.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.510][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-19 19:44:44.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-19 19:44:44.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.514][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-19 19:44:44.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-19 19:44:44.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.518][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-19 19:44:44.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-19 19:44:44.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:44.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:44.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:44.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:44.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:44.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:44.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:44.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:44.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:44.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:44.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:44.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:44.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:44.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:44.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:44.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:44.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:44.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:44.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:44.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:44.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.635][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:44.636][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:44.637][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.638][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:44.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:44.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.654][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.670][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.674][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.676][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.676][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.677][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:44.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.692][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:44.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:44.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.697][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:44.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:44.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:44.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:44.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.706][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:44.707][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:44.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.708][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.710][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:44.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:44.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.724][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:44.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:44.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.730][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:44.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:44.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.734][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:44.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:44.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.737][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:44.739][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:44.740][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.741][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.742][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:44.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:44.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.754][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:44.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:44.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.758][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:44.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:44.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:44.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:44.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.766][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:44.767][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:44.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.769][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:44.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:44.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:44.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:44.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:44.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:44.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.793][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:44.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:44.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.797][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:44.798][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:44.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.800][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:44.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:44.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.813][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:44.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:44.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.817][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:44.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:44.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.821][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:44.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:44.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.826][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:44.827][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:44.828][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.829][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.836][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:44.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:44.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.851][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-19 19:44:44.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:44.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.856][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-19 19:44:44.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:44.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.860][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-19 19:44:44.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:44.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.864][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-19 19:44:44.865][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:44.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.866][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.867][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-19 19:44:44.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:44.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.881][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:44.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:44.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.885][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:44.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:44.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.890][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:44.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:44.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.895][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:44.896][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:44.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.898][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.899][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:44.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:44.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.913][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:44.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:44.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.917][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:44.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:44.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.922][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:44.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:44.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.928][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:44.929][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:44.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.932][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.933][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:44.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:44.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.949][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:44.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:44.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.955][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:44.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:44.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.959][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:44.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:44.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.964][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:44.965][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:44.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.967][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.967][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:44.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:44.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.981][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:44.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:44.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.986][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:44.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:44.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.990][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:44.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:44.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.994][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:44.996][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:44.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:44.998][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:44.999][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:45.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:45.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.023][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:45.025][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:45.026][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.027][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.032][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:45.034][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:45.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.036][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.042][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:45.043][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:45.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.046][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.052][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:45.053][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:45.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.055][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.062][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:45.063][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:45.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.065][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.071][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:45.073][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:45.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.075][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.081][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:45.083][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:45.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.085][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.091][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:45.092][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:45.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.094][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.101][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-19 19:44:45.102][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:45.103][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.103][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.109][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:45.111][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:45.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.112][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.119][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:45.120][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:45.122][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.122][ef$get] fields variable is a list.
biodb.INFO [2025-03-19 19:44:45.133][biodb::testThat]
biodb.INFO [2025-03-19 19:44:45.135][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-19 19:44:45.136][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:44:45.137][biodb::testThat]
biodb.DEBUG[2025-03-19 19:44:45.154][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-03-19 19:44:45.161][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:44:45.166][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-03-19 19:44:45.168][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:44:45.169][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-03-19 19:44:45.170][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:44:45.207][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:44:45.209][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:44:45.212][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:45.213][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:45.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:45.221][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:45.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:45.223][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:45.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:44:45.228][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:45.229][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:45.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.231][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:45.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:45.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.260][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:45.261][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:45.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.263][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.264][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:45.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:45.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.269][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:45.271][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:45.272][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.273][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.274][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:45.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:45.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.278][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:45.279][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:45.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.280][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.282][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:45.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:45.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.286][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:45.287][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:45.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.289][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.290][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:45.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:45.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.294][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:45.296][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:45.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.298][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.299][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:45.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:45.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.304][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:44:45.305][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:45.306][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.307][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.308][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:44:45.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:45.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.313][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:45.314][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:45.315][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.316][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:45.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:45.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.322][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:45.324][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:45.325][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.326][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.329][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:45.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:45.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.333][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:45.335][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:45.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.337][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.338][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:45.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:45.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.343][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:45.344][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:45.345][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.346][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.348][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:45.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:45.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:45.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:45.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.359][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:45.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:45.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:45.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:45.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.374][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:45.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:45.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:45.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:45.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:45.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:45.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:45.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:45.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:45.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:45.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:45.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:45.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:45.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:45.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:45.404][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-03-19 19:44:45.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-19 19:44:45.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-19 19:44:45.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-19 19:44:45.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-19 19:44:45.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-19 19:44:45.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-19 19:44:45.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-19 19:44:45.430][biodb::testThat]
biodb.INFO [2025-03-19 19:44:45.432][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-19 19:44:45.433][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:44:45.435][biodb::testThat]
biodb.TRACE[2025-03-19 19:44:45.439][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:45.440][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:45.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.443][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:45.444][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-03-19 19:44:45.476][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:45.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:45.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.482][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:45.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:45.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.488][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:45.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:45.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:45.494][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-03-19 19:44:45.500][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-19 19:44:45.526][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:44:45.549][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-19 19:44:45.551][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:44:45.554][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-19 19:44:45.584][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:44:45.589][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:44:45.591][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-19 19:44:45.593][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:44:45.595][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-19 19:44:45.597][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-03-19 19:44:45.614][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:45.615][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:45.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.617][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.619][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:45.620][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:45.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.622][ef$get] fields variable is a list.
biodb.INFO [2025-03-19 19:44:45.628][biodb::testThat]
biodb.INFO [2025-03-19 19:44:45.629][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-03-19 19:44:45.631][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:44:45.631][biodb::testThat]
biodb.TRACE[2025-03-19 19:44:45.665][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:45.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:45.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.671][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:45.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:45.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.676][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:45.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:45.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:45.753][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:44:45.757][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:44:45.759][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-19 19:44:45.760][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:44:45.762][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-03-19 19:44:45.783][biodb::testThat]
biodb.INFO [2025-03-19 19:44:45.785][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-03-19 19:44:45.786][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:44:45.788][biodb::testThat]
biodb.TRACE[2025-03-19 19:44:45.816][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:45.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:45.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.821][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:45.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:45.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.827][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:45.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:45.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.832][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:45.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:45.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.836][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:45.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:45.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.841][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:45.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:45.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.846][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-19 19:44:45.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-19 19:44:45.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.851][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-19 19:44:45.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-19 19:44:45.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.855][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-19 19:44:45.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-19 19:44:45.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.860][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-19 19:44:45.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-19 19:44:45.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:45.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:45.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.898][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:45.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:45.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.902][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:45.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:45.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.905][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:45.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:45.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.910][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:45.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:45.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:45.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:45.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.919][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-19 19:44:45.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-19 19:44:45.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.924][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-19 19:44:45.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-19 19:44:45.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.929][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-19 19:44:45.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-19 19:44:45.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:45.934][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-19 19:44:45.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-19 19:44:45.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:45.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-19 19:44:45.945][biodb::testThat]
biodb.INFO [2025-03-19 19:44:45.946][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-19 19:44:45.948][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:44:45.949][biodb::testThat]
biodb.INFO [2025-03-19 19:44:45.960][biodb::testThat]
biodb.INFO [2025-03-19 19:44:45.961][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-19 19:44:45.962][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:44:45.964][biodb::testThat]
biodb.INFO [2025-03-19 19:44:45.975][biodb::testThat]
biodb.INFO [2025-03-19 19:44:45.977][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-19 19:44:45.978][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:44:45.979][biodb::testThat]
biodb.DEBUG[2025-03-19 19:44:45.983][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-03-19 19:44:46.693][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-03-19 19:44:47.827][biodb::testThat]
biodb.INFO [2025-03-19 19:44:47.828][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-19 19:44:47.830][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:44:47.831][biodb::testThat]
biodb.DEBUG[2025-03-19 19:44:48.424][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2025-03-19 19:44:48.830][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:48.832][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:48.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:48.835][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:48.836][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:48.838][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:48.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:48.840][ef$get] fields variable is a list.
biodb.INFO [2025-03-19 19:44:48.842][biodb::testThat]
biodb.INFO [2025-03-19 19:44:48.843][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2025-03-19 19:44:48.844][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:44:48.845][biodb::testThat]
biodb.TRACE[2025-03-19 19:44:48.860][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:48.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:48.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:48.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:48.878][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:48.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:48.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:48.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:48.882][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:48.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:48.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:48.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:48.978][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:44:48.983][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:44:48.985][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-19 19:44:48.987][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:44:48.989][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-19 19:44:49.071][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:44:49.075][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:44:49.076][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-19 19:44:49.077][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:44:49.079][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-03-19 19:44:49.097][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-19 19:44:49.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-19 19:44:49.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:49.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:49.109][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:49.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:49.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:49.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:49.113][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:49.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:49.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:49.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:49.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:49.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:49.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:49.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:49.126][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:49.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:49.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:49.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:49.131][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:49.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:49.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:49.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:49.143][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:44:49.148][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:44:49.149][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-19 19:44:49.151][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:44:49.153][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-19 19:44:49.156][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:49.157][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:49.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:49.166][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:49.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:49.168][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:49.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:49.171][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-03-19 19:44:49.234][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:44:49.237][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-03-19 19:44:49.239][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:44:49.240][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:44:49.242][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:44:49.243][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:44:49.245][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:44:49.255][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:44:49.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:49.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:49.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:49.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:49.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:49.272][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:49.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:49.275][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-03-19 19:44:49.279][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:44:49.280][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:44:49.282][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-03-19 19:44:49.895][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-03-19 19:44:50.259][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:44:50.262][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-03-19 19:44:50.281][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-03-19 19:44:50.285][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-03-19 19:44:50.287][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:44:50.289][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:44:50.291][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:44:50.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:50.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:50.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:50.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:50.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:50.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:50.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:44:50.308][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:50.309][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:50.310][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.311][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:50.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:50.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.318][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:50.319][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:50.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.321][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.323][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:50.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:50.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.328][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:50.330][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:50.331][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.332][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.333][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:50.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:50.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.338][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:50.339][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:50.340][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.341][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.343][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:50.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:50.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.348][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:50.349][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:50.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.352][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.353][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:50.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:50.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.371][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:50.373][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:50.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.375][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.377][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:44:50.378][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:50.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.380][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.382][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:44:50.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:50.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.386][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:50.387][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:50.389][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.390][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:50.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:50.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.396][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:50.398][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:50.399][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.400][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.401][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:50.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:50.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.406][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:50.407][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:50.408][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.409][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.410][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:50.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:50.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.415][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:50.416][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:50.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.418][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.419][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:50.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:50.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:50.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:50.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.427][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:50.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:50.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:50.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:50.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:50.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:50.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:50.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:50.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:50.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:50.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:50.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:50.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:50.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:50.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:50.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:50.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:50.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:50.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:50.466][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-03-19 19:44:50.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:50.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:50.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.489][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:50.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:50.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:50.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:50.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:50.500][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:44:50.503][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:44:50.505][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-19 19:44:50.506][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:44:50.508][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-19 19:44:50.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:50.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:50.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:50.534][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:50.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:50.536][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:50.538][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[2025-03-19 19:44:50.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:50.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:50.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:50.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:50.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:50.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:50.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:50.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:50.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:50.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:50.556][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:50.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:50.564][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:50.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:50.566][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:50.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:50.568][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-03-19 19:44:50.570][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:44:50.572][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-03-19 19:44:50.573][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:44:50.574][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:44:50.576][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:44:50.577][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:44:50.578][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:44:50.579][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:44:50.600][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:50.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:50.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:50.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:50.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:50.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:50.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:50.615][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-03-19 19:44:50.638][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:44:50.640][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:44:50.662][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-03-19 19:44:51.021][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-03-19 19:44:51.383][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:44:51.386][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-03-19 19:44:51.390][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-03-19 19:44:51.393][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-03-19 19:44:51.395][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:44:51.397][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:44:51.399][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:44:51.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:51.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:51.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:51.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:51.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:51.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:51.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:44:51.417][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:51.418][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:51.420][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.420][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:51.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:51.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.425][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:51.432][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:51.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.438][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.439][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:51.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:51.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.444][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:51.445][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:51.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.447][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.448][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:51.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:51.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.452][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:51.453][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:51.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.455][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.456][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:51.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:51.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.461][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:51.463][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:51.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.465][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.466][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:51.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:51.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.471][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:51.472][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:51.473][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.474][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.475][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:44:51.477][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:51.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.479][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.480][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:44:51.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:51.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.484][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:51.485][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:51.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.487][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.489][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:51.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:51.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.493][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:51.494][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:51.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.496][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.497][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:51.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:51.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.501][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:51.503][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:51.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.505][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.507][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:51.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:51.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.512][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:51.513][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:51.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.515][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.517][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:51.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:51.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:51.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:51.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:51.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:51.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:51.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:51.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:51.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:51.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:51.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:51.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:51.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:51.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:51.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:51.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:51.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:51.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:51.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:51.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:51.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:51.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:51.571][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-03-19 19:44:51.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:51.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:51.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.577][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:51.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:51.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.581][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:51.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:51.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:51.611][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:44:51.615][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:44:51.617][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-19 19:44:51.619][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:44:51.621][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-19 19:44:51.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:51.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:51.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:51.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:51.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:51.634][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:51.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:44:51.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:51.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:51.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:51.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:51.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:51.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:51.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:51.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:51.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:51.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:51.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:51.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:51.658][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:51.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:51.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:51.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:51.664][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-03-19 19:44:51.665][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:44:51.703][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-03-19 19:44:51.705][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:44:51.706][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:44:51.708][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:44:51.709][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:44:51.710][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:44:51.711][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:44:51.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:51.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:51.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:51.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:51.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:51.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:51.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:51.726][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-03-19 19:44:51.729][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:44:51.730][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:44:51.731][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-03-19 19:44:52.091][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-03-19 19:44:52.455][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:44:52.458][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-03-19 19:44:52.462][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-03-19 19:44:52.466][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-03-19 19:44:52.468][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:44:52.470][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:44:52.471][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:44:52.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:52.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:52.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:52.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:52.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:52.483][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:52.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:44:52.487][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:52.488][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:52.489][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.490][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:52.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:52.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.496][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:52.497][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:52.498][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.499][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.501][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:52.502][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:52.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.505][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.507][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:52.508][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:52.509][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.510][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.511][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:52.512][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:52.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.514][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.515][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:52.516][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:52.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.518][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.520][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:44:52.521][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:52.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.524][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.525][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:52.527][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:52.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.529][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.531][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:52.532][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:52.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.534][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.536][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:52.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:52.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.540][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:52.550][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:52.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.554][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.556][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:52.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:52.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.560][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:52.561][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:52.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.564][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:52.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:52.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:52.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:52.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:52.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:52.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:52.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:52.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:52.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:52.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:52.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:52.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:52.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:52.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:52.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:52.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:52.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:52.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:52.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:52.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:52.610][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-03-19 19:44:52.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:52.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:52.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.615][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:52.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:52.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.618][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:52.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:52.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:52.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:52.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:52.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:52.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:52.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:52.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:52.631][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:52.631][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:52.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:52.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:52.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:52.640][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:52.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:52.643][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-03-19 19:44:52.644][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:44:52.645][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-03-19 19:44:52.647][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:44:52.649][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:44:52.651][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:44:52.652][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:44:52.654][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:44:52.655][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:44:52.658][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:52.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:52.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:52.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:52.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:52.680][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:52.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:52.682][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-03-19 19:44:52.686][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:44:52.687][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:44:52.689][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-03-19 19:44:53.051][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-03-19 19:44:53.490][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:44:53.492][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-03-19 19:44:53.496][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-03-19 19:44:53.499][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-03-19 19:44:53.502][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:44:53.503][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:44:53.505][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:44:53.507][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:53.509][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:53.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:53.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:53.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:53.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:53.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:44:53.522][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:53.523][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:53.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.525][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:53.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:53.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.530][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:53.531][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:53.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.533][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.534][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:53.535][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:53.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.537][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.539][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:53.540][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:53.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.543][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.545][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:53.546][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:53.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.549][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.550][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:53.552][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:53.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.554][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.556][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:44:53.557][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:53.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.560][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.562][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:53.564][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:53.566][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.568][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.570][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:53.572][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:53.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.577][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.579][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:53.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:53.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.584][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:53.586][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:53.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.589][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.590][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:53.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:53.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.595][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:53.596][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:53.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.599][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:53.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:53.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:53.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:53.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:53.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:53.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:53.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:53.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:53.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:53.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:53.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:53.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:53.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:53.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:53.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:53.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:53.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:53.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:53.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:53.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:53.656][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-03-19 19:44:53.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:53.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:53.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.662][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:53.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:53.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:53.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:53.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:53.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:53.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:53.675][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:53.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:53.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:53.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:53.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:53.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:53.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:53.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:53.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:53.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:53.689][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.DEBUG[2025-03-19 19:44:53.691][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-03-19 19:44:53.692][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:44:53.694][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-03-19 19:44:53.696][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:44:53.697][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:44:53.698][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:44:53.699][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:44:53.700][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:44:53.701][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:44:53.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:53.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:53.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:53.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:53.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:53.714][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:53.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:53.716][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-03-19 19:44:53.719][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:44:53.725][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:44:53.728][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-03-19 19:44:54.130][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-03-19 19:44:54.497][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:44:54.500][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-03-19 19:44:54.505][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-03-19 19:44:54.509][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-03-19 19:44:54.511][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:44:54.512][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:44:54.514][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:44:54.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:54.516][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:54.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:54.522][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:54.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:54.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:54.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:44:54.529][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:54.531][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:54.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.533][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:54.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:54.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.539][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:54.540][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:54.541][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.542][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.543][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:54.545][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:54.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.547][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.549][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:54.550][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:54.551][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.552][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.554][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:54.554][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:54.555][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.556][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.557][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:54.558][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:54.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.561][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.562][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:44:54.563][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:54.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.565][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.566][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:54.567][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:54.568][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.569][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.570][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:54.571][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:54.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.573][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.576][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:54.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:54.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.580][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:54.581][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:54.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.584][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.585][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:54.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:54.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.591][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:54.592][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:54.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.594][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:54.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:54.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:54.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:54.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:54.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:54.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:54.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:54.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:54.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:54.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:54.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:54.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:54.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:54.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:54.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:54.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:54.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:54.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:54.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:54.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:54.655][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-03-19 19:44:54.656][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:54.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:54.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:54.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:54.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:54.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:54.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.671][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:54.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:54.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:54.676][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:54.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:54.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:54.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:54.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:54.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:54.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:54.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:54.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:54.693][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:54.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:54.696][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-03-19 19:44:54.697][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:44:54.700][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-03-19 19:44:54.701][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:44:54.703][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:44:54.704][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:44:54.705][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:44:54.707][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:44:54.708][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:44:54.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:54.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:54.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:54.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:54.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:54.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:54.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:54.726][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-03-19 19:44:54.730][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:44:54.731][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:44:54.733][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-03-19 19:44:55.093][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-03-19 19:44:55.470][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:44:55.473][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-03-19 19:44:55.483][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-03-19 19:44:55.490][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-03-19 19:44:55.492][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:44:55.494][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:44:55.495][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:44:55.497][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:55.498][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:55.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:55.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:55.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:55.508][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:55.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:44:55.511][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:55.512][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:55.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.514][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:55.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:55.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.519][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:55.520][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:55.521][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.522][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.523][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:55.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:55.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.527][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:55.528][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:55.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.530][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.531][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:55.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:55.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.535][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:55.536][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:55.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.538][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:55.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:55.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.543][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:55.544][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:55.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.546][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.548][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:55.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:55.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.553][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:55.555][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:55.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.557][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.559][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:55.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:55.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.563][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:44:55.563][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:55.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.565][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.566][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:44:55.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:55.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.571][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:55.572][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:55.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.574][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:55.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:55.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.581][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:55.582][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:55.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.584][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.586][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:55.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:55.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.590][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:55.591][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:55.592][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.599][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.600][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:55.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:55.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.606][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:55.607][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:55.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.609][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.611][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:55.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:55.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:55.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:55.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.619][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:55.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:55.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:55.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:55.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:55.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:55.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:55.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:55.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:55.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:55.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:55.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:55.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:55.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:55.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:55.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:55.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:55.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:55.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:55.659][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-03-19 19:44:55.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:55.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:55.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.664][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:55.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:55.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:55.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:55.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:55.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:55.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:55.673][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:55.674][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:55.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:55.682][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:55.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:55.685][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:55.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:55.688][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-03-19 19:44:55.690][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:44:55.692][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-03-19 19:44:55.694][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:44:55.695][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:44:55.696][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:44:55.697][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:44:55.698][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:44:55.699][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:44:55.702][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:55.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:55.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:55.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:55.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:55.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:55.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:55.721][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-03-19 19:44:55.724][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:44:55.725][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:44:55.727][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-03-19 19:44:56.094][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-03-19 19:44:56.475][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:44:56.478][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-03-19 19:44:56.482][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-03-19 19:44:56.485][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-03-19 19:44:56.486][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:44:56.488][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:44:56.490][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:44:56.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:56.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:56.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:56.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:56.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:56.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:56.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:44:56.508][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:56.509][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:56.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.511][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:56.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:56.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.517][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:56.517][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:56.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.519][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.521][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:56.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:56.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.526][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:56.527][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:56.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.529][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.531][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:56.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:56.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.535][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:56.536][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:56.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.538][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.540][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:56.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:56.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.544][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:56.546][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:56.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.548][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.549][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:56.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:56.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.554][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:56.555][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:56.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.558][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.559][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:56.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:56.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.565][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:44:56.566][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:56.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.568][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.569][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:44:56.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:56.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.575][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:56.576][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:56.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.578][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:56.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:56.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.597][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:56.599][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:56.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.601][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.603][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:56.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:56.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.609][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:56.610][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:56.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.612][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.614][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:56.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:56.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.618][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:56.620][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:56.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.622][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.624][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:56.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:56.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:56.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:56.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:56.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:56.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:56.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:56.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:56.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:56.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:56.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:56.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:56.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:56.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:56.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:56.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:56.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:56.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:56.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:56.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:56.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:56.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:56.673][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-03-19 19:44:56.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:56.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:56.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.679][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:56.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:56.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:56.684][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:56.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:56.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:56.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:56.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:56.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:56.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:56.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:56.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:56.700][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:56.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:56.703][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-03-19 19:44:56.704][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:44:56.706][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-03-19 19:44:56.708][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:44:56.716][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:44:56.718][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:44:56.719][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:44:56.720][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:44:56.722][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:44:56.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:56.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:56.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:56.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:56.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:56.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:56.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:56.739][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-03-19 19:44:56.742][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:44:56.744][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:44:56.745][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-03-19 19:44:57.103][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-03-19 19:44:57.467][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:44:57.469][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-03-19 19:44:57.473][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-03-19 19:44:57.477][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-03-19 19:44:57.479][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:44:57.481][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:44:57.482][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:44:57.484][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:57.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:57.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:57.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:57.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:57.495][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:57.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:44:57.499][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:57.500][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:57.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.503][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:57.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:57.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.508][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:57.510][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:57.511][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.512][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.514][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:57.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:57.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.519][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:57.520][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:57.521][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.522][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.523][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:57.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:57.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.527][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:57.529][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:57.530][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.531][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.532][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:57.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:57.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.536][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:57.537][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:57.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.539][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.540][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:57.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:57.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.544][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:57.545][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:57.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.547][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.549][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:44:57.550][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:57.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.562][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.563][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:44:57.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:57.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.568][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:57.569][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:57.570][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.571][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:57.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:57.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.577][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:57.578][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:57.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.580][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.581][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:57.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:57.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.585][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:57.586][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:57.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.588][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.589][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:57.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:57.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.593][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:57.595][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:57.596][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.597][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.599][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:57.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:57.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:57.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:57.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.607][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:57.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:57.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:57.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:57.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:57.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:57.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:57.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:57.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:57.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:57.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:57.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:57.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:57.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:57.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:57.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:57.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:57.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:57.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:57.643][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-03-19 19:44:57.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:57.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:57.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.647][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:57.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:57.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:57.651][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:57.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:57.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:57.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:57.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:57.656][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:57.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:57.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:57.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:57.671][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:57.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:57.674][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-03-19 19:44:57.675][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:44:57.676][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-03-19 19:44:57.678][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:44:57.679][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:44:57.681][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:44:57.682][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:44:57.683][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:44:57.684][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:44:57.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:57.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:57.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:57.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:57.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:57.700][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:57.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:57.702][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-03-19 19:44:57.706][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:44:57.707][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:44:57.708][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-03-19 19:44:58.077][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-03-19 19:44:58.446][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:44:58.449][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-03-19 19:44:58.453][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-03-19 19:44:58.456][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-03-19 19:44:58.458][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:44:58.460][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:44:58.461][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:44:58.463][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:58.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:58.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:58.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:58.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:58.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:58.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:44:58.478][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:58.479][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:58.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.481][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:58.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:58.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.486][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:58.487][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:58.488][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.489][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.490][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:58.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:58.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.494][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:58.495][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:58.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.497][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.499][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:58.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:58.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.503][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:58.504][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:58.505][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.506][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.507][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:58.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:58.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.511][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:58.512][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:58.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.523][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.525][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:58.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:58.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.531][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:58.532][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:58.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.534][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.535][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:44:58.536][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:58.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.538][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.540][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:44:58.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:58.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.545][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:58.546][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:58.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.549][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:58.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:58.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.555][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:58.556][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:58.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.558][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.560][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:58.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:58.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.565][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:58.566][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:58.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.568][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.569][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:58.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:58.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.573][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:58.574][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:58.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.576][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.577][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:58.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:58.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:58.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:58.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:58.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:58.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:58.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:58.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:58.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:58.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:58.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:58.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:58.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:58.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:58.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:58.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:58.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:58.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:58.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:58.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:58.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:58.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:58.624][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-03-19 19:44:58.625][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:58.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:58.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:58.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:58.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:58.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:58.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:58.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:58.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:58.645][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:58.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:58.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:58.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:58.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:58.656][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:58.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:58.658][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-03-19 19:44:58.659][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:44:58.661][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-03-19 19:44:58.662][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:44:58.663][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:44:58.664][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:44:58.665][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:44:58.666][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:44:58.667][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:44:58.669][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:58.670][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:58.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:58.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:58.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:58.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:58.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:58.681][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-03-19 19:44:58.684][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:44:58.685][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:44:58.687][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-03-19 19:44:59.055][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-03-19 19:44:59.421][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:44:59.424][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-03-19 19:44:59.429][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-03-19 19:44:59.434][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-03-19 19:44:59.436][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:44:59.438][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:44:59.439][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:44:59.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:59.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:59.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:59.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:59.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:59.452][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:59.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:44:59.456][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:59.457][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:59.458][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.459][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:59.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:59.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.466][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:59.467][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:59.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.469][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.470][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:44:59.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:44:59.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.474][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:59.475][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:59.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.476][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.477][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:44:59.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:44:59.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.490][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:59.491][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:59.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.493][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:44:59.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:44:59.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.498][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:59.499][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:59.500][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.501][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.503][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:44:59.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:44:59.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.506][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:59.507][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:44:59.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.510][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.511][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:44:59.512][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:59.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.514][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.515][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:44:59.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:59.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.519][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:59.521][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:59.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.523][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:59.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:44:59.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.528][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:59.529][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:59.530][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.531][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.533][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:44:59.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:44:59.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.536][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:59.537][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:59.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.539][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.541][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:44:59.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:44:59.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.545][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:59.547][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:59.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.548][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.549][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:44:59.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:44:59.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:59.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:59.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:59.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:59.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:59.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:59.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:44:59.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:44:59.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:59.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:59.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:59.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:59.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:59.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:59.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:59.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:59.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:59.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:59.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:44:59.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:44:59.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:59.607][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-03-19 19:44:59.607][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:59.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:59.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.613][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:59.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:59.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:44:59.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:59.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:44:59.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:44:59.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:44:59.623][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:59.624][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:59.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:59.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:59.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:59.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:59.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:59.636][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-03-19 19:44:59.637][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:44:59.639][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-03-19 19:44:59.640][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:44:59.641][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:44:59.642][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:44:59.643][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:44:59.645][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:44:59.646][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:44:59.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:44:59.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:44:59.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:44:59.658][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:44:59.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:44:59.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:44:59.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:44:59.662][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-03-19 19:44:59.665][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:44:59.666][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:44:59.667][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-03-19 19:45:00.030][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-03-19 19:45:00.415][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:00.418][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-03-19 19:45:00.422][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-03-19 19:45:00.426][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-03-19 19:45:00.428][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:45:00.429][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:45:00.430][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:45:00.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:00.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:00.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:00.439][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:00.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:00.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:00.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:00.445][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:00.446][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:00.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.448][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:00.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:00.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.460][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:00.465][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:00.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.467][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.469][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:00.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:00.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.473][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:00.475][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:00.476][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.477][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.479][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:00.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:00.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.483][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:00.484][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:00.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.486][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.487][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:00.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:00.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.492][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:00.493][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:00.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.496][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.497][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:00.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:00.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.501][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:00.502][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:00.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.504][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.505][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:00.506][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:00.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.508][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.510][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:00.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:00.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.514][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:00.515][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:00.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.517][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:00.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:00.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.523][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:00.524][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:00.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.525][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.527][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:00.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:00.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.531][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:00.532][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:00.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.533][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.535][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:00.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:00.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.539][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:00.540][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:00.541][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.542][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.543][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:00.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:00.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:00.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:00.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:00.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:00.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:00.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:00.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:00.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:00.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:00.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:00.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:00.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:00.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:00.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:00.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:00.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:00.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:00.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:00.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:00.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:00.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:00.596][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-03-19 19:45:00.597][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:00.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:00.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.601][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:00.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:00.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:00.604][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:00.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:00.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:00.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:00.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:00.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:00.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:00.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:00.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:00.619][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:00.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:00.620][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-03-19 19:45:00.622][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:45:00.623][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-03-19 19:45:00.625][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:45:00.626][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:45:00.627][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:45:00.628][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:45:00.629][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:45:00.629][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:45:00.632][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:00.632][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:00.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:00.639][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:00.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:00.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:00.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:00.643][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-03-19 19:45:00.646][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:00.647][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:00.648][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-03-19 19:45:01.007][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-03-19 19:45:01.375][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:01.378][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-03-19 19:45:01.383][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-03-19 19:45:01.387][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-03-19 19:45:01.389][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:45:01.390][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:45:01.392][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:45:01.394][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:01.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:01.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:01.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:01.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:01.416][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:01.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:01.421][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:01.422][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:01.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.425][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:01.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:01.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.431][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:01.432][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:01.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.435][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.436][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:01.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:01.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.441][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:01.443][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:01.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.445][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.446][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:01.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:01.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.452][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:01.453][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:01.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.456][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.457][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:01.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:01.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.461][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:01.462][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:01.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.464][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.465][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:01.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:01.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.470][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:01.471][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:01.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.473][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.475][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:01.476][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:01.477][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.479][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.480][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:01.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:01.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.485][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:01.486][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:01.488][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.489][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:01.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:01.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.496][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:01.497][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:01.498][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.499][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.501][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:01.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:01.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.506][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:01.507][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:01.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.508][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.510][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:01.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:01.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.514][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:01.515][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:01.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.516][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.517][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:01.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:01.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:01.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:01.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:01.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:01.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:01.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:01.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:01.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:01.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:01.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:01.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:01.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:01.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:01.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:01.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:01.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:01.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:01.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:01.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:01.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:01.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:01.570][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-03-19 19:45:01.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:01.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:01.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.576][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:01.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:01.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:01.580][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:01.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:01.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:01.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:01.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:01.586][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:01.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:01.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:01.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:01.598][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:01.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:01.601][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-03-19 19:45:01.602][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:45:01.603][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-03-19 19:45:01.605][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:45:01.606][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:45:01.607][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:45:01.608][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:45:01.609][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:45:01.610][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:45:01.613][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:01.614][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:01.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:01.620][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:01.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:01.622][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:01.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:01.624][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-03-19 19:45:01.627][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:01.629][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:01.630][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-03-19 19:45:01.991][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-03-19 19:45:02.639][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:02.642][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-03-19 19:45:02.658][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-03-19 19:45:02.661][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-03-19 19:45:02.664][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:45:02.665][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:45:02.666][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:45:02.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:02.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:02.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:02.676][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:02.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:02.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:02.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:02.681][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:02.682][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:02.683][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.684][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:02.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:02.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.690][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:02.691][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:02.692][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.693][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.695][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:02.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:02.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.699][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:02.701][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:02.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.702][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.704][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:02.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:02.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.709][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:02.711][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:02.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.712][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.714][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:02.714][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:02.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.716][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.718][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:02.719][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:02.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.721][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.722][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:02.723][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:02.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.725][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.726][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:02.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:02.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.730][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:02.731][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:02.732][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.733][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:02.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:02.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.739][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:02.740][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:02.741][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.742][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.744][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:02.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:02.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.748][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:02.749][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:02.750][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.751][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.753][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:02.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:02.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.756][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:02.757][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:02.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.759][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.760][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:02.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:02.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:02.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:02.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:02.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:02.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:02.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:02.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:02.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:02.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:02.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:02.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:02.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:02.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:02.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:02.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:02.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:02.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:02.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:02.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:02.805][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-03-19 19:45:02.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:02.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:02.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:02.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:02.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:02.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:02.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:02.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:02.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:02.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:02.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:02.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:02.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:02.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:02.831][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:02.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:02.833][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-03-19 19:45:02.834][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:45:02.835][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-03-19 19:45:02.836][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:45:02.837][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:45:02.839][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:45:02.840][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:45:02.842][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:45:02.843][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:45:02.846][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:02.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:02.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:02.854][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:02.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:02.856][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:02.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:02.858][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-03-19 19:45:02.861][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:02.862][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:02.863][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-03-19 19:45:03.226][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-03-19 19:45:03.587][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:03.589][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-03-19 19:45:03.603][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-03-19 19:45:03.607][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-03-19 19:45:03.609][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:45:03.611][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:45:03.612][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:45:03.614][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:03.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:03.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:03.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:03.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:03.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:03.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:03.627][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:03.629][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:03.630][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.631][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:03.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:03.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.638][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:03.639][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:03.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.641][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.643][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:03.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:03.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.647][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:03.648][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:03.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.650][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.652][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:03.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:03.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.658][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:03.659][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:03.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.661][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.663][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:03.664][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:03.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.667][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.668][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:03.670][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:03.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.672][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.673][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:03.674][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:03.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.676][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.677][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:03.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:03.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.680][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:03.681][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:03.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.683][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.684][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:03.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:03.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.689][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:03.690][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:03.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.692][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.694][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:03.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:03.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.699][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:03.701][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:03.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.703][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.704][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:03.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:03.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.708][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:03.709][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:03.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.711][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:03.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:03.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:03.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:03.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:03.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:03.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.732][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:03.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:03.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:03.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:03.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:03.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:03.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:03.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:03.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:03.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:03.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:03.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:03.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:03.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:03.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:03.761][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-03-19 19:45:03.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:03.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:03.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:03.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:03.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:03.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:03.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:03.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:03.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:03.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:03.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:03.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:03.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:03.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:03.783][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:03.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:03.785][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-03-19 19:45:03.787][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:45:03.789][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-03-19 19:45:03.791][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:45:03.792][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:45:03.793][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:45:03.795][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:45:03.795][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:45:03.796][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:45:03.799][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:03.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:03.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:03.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:03.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:03.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:03.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:03.813][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-03-19 19:45:03.817][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:03.818][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:03.819][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-03-19 19:45:04.172][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-03-19 19:45:04.533][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:04.535][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-03-19 19:45:04.550][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-03-19 19:45:04.554][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-03-19 19:45:04.556][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:45:04.558][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:45:04.559][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:45:04.561][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:04.562][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:04.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:04.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:04.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:04.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:04.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:04.574][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:04.576][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:04.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.578][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:04.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:04.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.583][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:04.584][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:04.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.586][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.587][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:04.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:04.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.591][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:04.592][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:04.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.594][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.595][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:04.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:04.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.600][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:04.601][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:04.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.602][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.604][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:04.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:04.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.609][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:04.610][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:04.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.612][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.614][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:04.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:04.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.618][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:04.619][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:04.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.621][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.622][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:04.623][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:04.625][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.626][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.627][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:04.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:04.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.631][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:04.632][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:04.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.634][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:04.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:04.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.639][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:04.641][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:04.642][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.643][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.644][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:04.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:04.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.649][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:04.650][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:04.651][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.652][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.654][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:04.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:04.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.665][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:04.666][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:04.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.669][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.670][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:04.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:04.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:04.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:04.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:04.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:04.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:04.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:04.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.686][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:04.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:04.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:04.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:04.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:04.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:04.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:04.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:04.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:04.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:04.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:04.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:04.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:04.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:04.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:04.714][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-03-19 19:45:04.715][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:04.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:04.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.718][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:04.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:04.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:04.722][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:04.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:04.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:04.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:04.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:04.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:04.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:04.733][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:04.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:04.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:04.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:04.738][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-03-19 19:45:04.739][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:45:04.742][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-03-19 19:45:04.743][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:45:04.744][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:45:04.745][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:45:04.746][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:45:04.747][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:45:04.748][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:45:04.751][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:04.753][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:04.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:04.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:04.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:04.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:04.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:04.771][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-03-19 19:45:04.775][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:04.776][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:04.778][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-03-19 19:45:05.145][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-03-19 19:45:05.541][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:05.544][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-03-19 19:45:05.550][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-03-19 19:45:05.553][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-03-19 19:45:05.555][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:45:05.556][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:45:05.558][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:45:05.559][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:05.560][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:05.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:05.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:05.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:05.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:05.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:05.572][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:05.573][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:05.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.574][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:05.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:05.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.579][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:05.580][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:05.581][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.582][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.583][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:05.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:05.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.586][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:05.587][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:05.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.589][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.590][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:05.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:05.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.594][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:05.595][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:05.596][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.596][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.597][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:05.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:05.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.601][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:05.602][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:05.603][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.604][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.605][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:05.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:05.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.610][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:05.612][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:05.613][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.613][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.615][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:05.617][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:05.618][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.619][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.621][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:05.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:05.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.626][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:05.627][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:05.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.629][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:05.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:05.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.634][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:05.643][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:05.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.647][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.648][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:05.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:05.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.652][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:05.653][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:05.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.657][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.659][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:05.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:05.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.662][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:05.663][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:05.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.665][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.666][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:05.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:05.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:05.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:05.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.675][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:05.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:05.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:05.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:05.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:05.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:05.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:05.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:05.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:05.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:05.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:05.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:05.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:05.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:05.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:05.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:05.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:05.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:05.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:05.714][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-03-19 19:45:05.715][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:05.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:05.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.719][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:05.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:05.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:05.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:05.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:05.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:05.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:05.727][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:05.728][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:05.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:05.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:05.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:05.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:05.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:05.741][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-03-19 19:45:05.743][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:45:05.744][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-03-19 19:45:05.746][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:45:05.747][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:45:05.749][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:45:05.754][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:45:05.756][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:45:05.757][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:45:05.761][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:05.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:05.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:05.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:05.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:05.772][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:05.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:05.774][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-03-19 19:45:05.778][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:05.779][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:05.780][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-03-19 19:45:06.143][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-03-19 19:45:06.511][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:06.514][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-03-19 19:45:06.520][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-03-19 19:45:06.523][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-03-19 19:45:06.525][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:45:06.526][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:45:06.528][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:45:06.529][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:06.530][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:06.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:06.537][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:06.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:06.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:06.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:06.544][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:06.546][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:06.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.548][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:06.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:06.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.554][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:06.555][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:06.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.558][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.560][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:06.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:06.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.564][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:06.566][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:06.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.568][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.570][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:06.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:06.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.574][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:06.576][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:06.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.578][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.580][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:06.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:06.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.584][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:06.585][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:06.586][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.587][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:06.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:06.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.594][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:06.595][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:06.596][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.598][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.599][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:06.600][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:06.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.608][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.613][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:06.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:06.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.620][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:06.621][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:06.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.623][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.625][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:06.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:06.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.630][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:06.631][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:06.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.634][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.636][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:06.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:06.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.640][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:06.642][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:06.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.644][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.646][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:06.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:06.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.651][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:06.653][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:06.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.655][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.656][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:06.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:06.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:06.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:06.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.667][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:06.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:06.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:06.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:06.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:06.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:06.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:06.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:06.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:06.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:06.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:06.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:06.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:06.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:06.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:06.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:06.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:06.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:06.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:06.708][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-03-19 19:45:06.709][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:06.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:06.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:06.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:06.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:06.717][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:06.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:06.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:06.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:06.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:06.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:06.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:06.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:06.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:06.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:06.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:06.742][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-03-19 19:45:06.743][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:45:06.745][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-03-19 19:45:06.747][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:45:06.748][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:45:06.750][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:45:06.751][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:45:06.752][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:45:06.753][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:45:06.756][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:06.757][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:06.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:06.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:06.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:06.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:06.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:06.769][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-03-19 19:45:06.771][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:06.773][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:06.774][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-03-19 19:45:07.128][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-03-19 19:45:07.490][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:07.493][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-03-19 19:45:07.498][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-03-19 19:45:07.502][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-03-19 19:45:07.504][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:45:07.506][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:45:07.508][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:45:07.510][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:07.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:07.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:07.522][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:07.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:07.524][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:07.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:07.528][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:07.530][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:07.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.538][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:07.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:07.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.557][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:07.558][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:07.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.560][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.562][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:07.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:07.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.567][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:07.568][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:07.569][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.570][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.571][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:07.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:07.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.577][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:07.578][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:07.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.581][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.582][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:07.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:07.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.586][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:07.592][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:07.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.598][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.600][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:07.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:07.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.606][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:07.608][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:07.609][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.610][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.612][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:07.613][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:07.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.615][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.617][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:07.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:07.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.621][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:07.622][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:07.623][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.624][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:07.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:07.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.630][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:07.632][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:07.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.633][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.635][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:07.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:07.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.638][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:07.639][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:07.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.641][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.642][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:07.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:07.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.648][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:07.650][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:07.651][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.652][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.654][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:07.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:07.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:07.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:07.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:07.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:07.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:07.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:07.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:07.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:07.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:07.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:07.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:07.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:07.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:07.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:07.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:07.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:07.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:07.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:07.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:07.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:07.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:07.707][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-03-19 19:45:07.716][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:07.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:07.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:07.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:07.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:07.728][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:07.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:07.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:07.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:07.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:07.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:07.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:07.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:07.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:07.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:07.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:07.746][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-03-19 19:45:07.747][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:45:07.749][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-03-19 19:45:07.751][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:45:07.752][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:45:07.753][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:45:07.754][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:45:07.755][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:45:07.757][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:45:07.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:07.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:07.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:07.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:07.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:07.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:07.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:07.775][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-03-19 19:45:07.779][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:07.780][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:07.782][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-03-19 19:45:08.140][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-03-19 19:45:08.508][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:08.511][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-03-19 19:45:08.515][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-03-19 19:45:08.518][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-03-19 19:45:08.519][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:45:08.521][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:45:08.522][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:45:08.524][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:08.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:08.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:08.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:08.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:08.535][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:08.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:08.540][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:08.541][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:08.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.543][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:08.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:08.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.549][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:08.550][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:08.551][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.551][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.553][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:08.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:08.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.557][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:08.558][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:08.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.568][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.569][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:08.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:08.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.576][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:08.576][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:08.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.578][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.579][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:08.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:08.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.583][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:08.584][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:08.584][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.585][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:08.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:08.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.590][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:08.591][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:08.592][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.593][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.595][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:08.596][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:08.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.599][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.601][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:08.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:08.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.604][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:08.605][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:08.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.607][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:08.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:08.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.611][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:08.612][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:08.613][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.614][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.616][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:08.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:08.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.620][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:08.621][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:08.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.622][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.624][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:08.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:08.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.627][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:08.628][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:08.629][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.630][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.631][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:08.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:08.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:08.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:08.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:08.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:08.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:08.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:08.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:08.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:08.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:08.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:08.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:08.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:08.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:08.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:08.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:08.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:08.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:08.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:08.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:08.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:08.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:08.689][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-03-19 19:45:08.690][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:08.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:08.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.694][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:08.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:08.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:08.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:08.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:08.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:08.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:08.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:08.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:08.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:08.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:08.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:08.713][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:08.714][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[2025-03-19 19:45:08.715][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-03-19 19:45:08.716][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:45:08.718][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-03-19 19:45:08.720][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:45:08.721][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:45:08.723][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:45:08.724][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:45:08.725][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:45:08.726][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:45:08.730][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:08.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:08.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:08.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:08.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:08.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:08.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:08.743][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-03-19 19:45:08.745][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:08.746][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:08.747][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-03-19 19:45:09.113][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-03-19 19:45:09.466][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:09.470][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-03-19 19:45:09.475][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-03-19 19:45:09.478][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-03-19 19:45:09.481][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:45:09.482][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:45:09.483][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:45:09.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:09.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:09.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:09.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:09.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:09.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:09.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:09.501][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:09.502][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:09.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.505][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:09.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:09.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.523][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:09.524][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:09.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.527][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.528][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:09.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:09.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.533][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:09.534][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:09.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.537][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.538][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:09.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:09.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.543][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:09.544][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:09.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.546][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.547][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:09.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:09.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.551][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:09.552][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:09.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.553][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.554][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:09.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:09.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.559][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:09.560][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:09.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.562][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.563][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:09.564][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:09.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.566][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.568][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:09.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:09.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.572][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:09.574][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:09.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.576][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:09.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:09.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.581][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:09.582][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:09.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.585][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.586][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:09.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:09.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.591][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:09.592][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:09.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.594][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.596][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:09.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:09.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.600][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:09.601][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:09.603][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.604][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.605][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:09.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:09.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:09.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:09.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:09.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:09.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:09.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:09.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:09.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:09.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:09.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:09.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:09.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:09.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:09.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:09.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:09.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:09.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:09.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:09.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:09.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:09.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:09.656][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-03-19 19:45:09.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:09.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:09.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.662][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:09.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:09.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:09.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:09.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:09.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:09.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:09.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:09.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:09.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:09.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:09.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:09.680][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:09.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:09.682][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-03-19 19:45:09.683][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:45:09.684][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-03-19 19:45:09.686][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:45:09.687][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:45:09.688][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:45:09.690][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:45:09.691][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:45:09.692][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:45:09.694][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:09.695][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:09.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:09.701][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:09.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:09.703][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:09.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:09.705][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-03-19 19:45:09.707][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:09.708][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:09.709][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-03-19 19:45:10.065][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-03-19 19:45:10.436][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:10.440][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-03-19 19:45:10.444][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-03-19 19:45:10.446][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-03-19 19:45:10.448][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:45:10.449][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:45:10.462][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:45:10.464][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:10.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:10.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:10.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:10.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:10.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:10.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:10.478][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:10.479][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:10.479][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.480][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:10.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:10.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.486][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:10.487][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:10.488][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.489][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.491][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:10.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:10.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.494][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:10.495][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:10.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.497][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.498][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:10.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:10.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.502][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:10.503][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:10.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.504][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.505][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:10.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:10.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.510][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:10.511][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:10.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.513][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.514][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:10.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:10.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.518][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:10.519][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:10.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.521][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.522][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:10.523][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.525][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.526][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:10.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.530][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:10.531][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:10.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.533][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:10.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:10.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.539][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:10.540][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:10.541][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.542][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.544][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:10.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:10.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.548][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:10.549][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:10.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.551][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.552][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:10.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:10.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.557][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:10.558][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:10.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.566][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.568][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:10.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:10.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.573][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:10.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:10.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:10.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:10.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:10.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:10.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:10.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:10.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:10.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:10.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:10.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:10.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:10.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:10.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:10.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:10.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:10.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:10.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:10.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:10.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:10.620][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-03-19 19:45:10.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.625][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:10.660][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:10.664][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:45:10.665][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-19 19:45:10.667][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:45:10.669][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-19 19:45:10.673][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:10.674][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:10.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:10.682][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:10.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:10.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:10.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:10.694][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.705][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:10.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:10.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:10.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:10.720][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:10.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:10.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:10.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:10.726][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.731][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:10.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:10.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:10.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:10.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:10.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:10.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:10.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:10.760][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:10.785][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:10.786][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:10.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:10.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:10.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:10.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:10.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:10.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:10.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:10.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:10.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:10.835][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:10.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:10.837][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:10.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:10.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:10.854][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:10.855][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:10.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:10.862][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:10.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:10.864][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:10.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:10.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:10.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:10.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:10.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:10.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:10.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:10.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:10.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:10.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.894][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.898][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:10.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:10.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:10.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:10.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:10.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:10.912][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:10.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:10.914][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:10.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:10.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:10.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:11.106][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:11.107][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:11.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:11.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:11.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:11.116][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:11.117][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.TRACE[2025-03-19 19:45:11.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:11.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:11.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:11.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:11.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:11.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:11.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:11.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:11.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.151][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.155][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:11.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:11.161][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:11.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:11.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:11.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:11.171][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:11.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:11.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.178][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:11.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:11.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:11.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:11.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:11.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:11.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:11.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:11.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.202][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:11.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:11.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:11.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:11.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:11.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:11.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:11.220][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[2025-03-19 19:45:11.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:11.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:11.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:11.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:11.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:11.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:11.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:11.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:11.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.250][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:11.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:11.262][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:11.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:11.270][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:11.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:11.273][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:11.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:11.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:11.288][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:11.290][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:11.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:11.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:11.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:11.300][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:11.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:11.303][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.312][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:11.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:11.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:11.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:11.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:11.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:11.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:11.333][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.TRACE[2025-03-19 19:45:11.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.341][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:11.352][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:11.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:11.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:11.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:11.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:11.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:11.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:11.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.370][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:11.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:11.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:11.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:11.387][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:11.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:11.390][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:11.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:11.393][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:11.406][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:11.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:11.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:11.414][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:11.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:11.417][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:11.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:11.419][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.424][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:11.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:11.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:11.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:11.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:11.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.475][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:11.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:11.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:11.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:11.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:11.484][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:11.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:11.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:11.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:11.521][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:11.524][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:11.526][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:11.529][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-19 19:45:11.890][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-19 19:45:12.251][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:12.254][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-03-19 19:45:12.259][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-03-19 19:45:12.271][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:12.275][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:12.276][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:12.278][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-19 19:45:12.644][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-19 19:45:13.008][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:13.011][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-03-19 19:45:13.015][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-03-19 19:45:13.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:13.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:13.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:13.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:13.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:13.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:13.030][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.DEBUG[2025-03-19 19:45:13.031][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-03-19 19:45:13.032][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:45:13.034][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-03-19 19:45:13.035][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:45:13.036][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:45:13.038][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:45:13.038][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:45:13.040][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:45:13.041][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:45:13.044][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:13.045][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:13.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:13.052][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:13.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:13.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:13.054][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[2025-03-19 19:45:13.056][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-03-19 19:45:13.058][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:13.059][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:13.060][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-03-19 19:45:13.423][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-03-19 19:45:13.798][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:13.801][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-03-19 19:45:13.805][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-03-19 19:45:13.809][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-03-19 19:45:13.811][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:45:13.813][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:45:13.814][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:45:13.816][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:13.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:13.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:13.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:13.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:13.826][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:13.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:13.830][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:13.831][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:13.832][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.833][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:13.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:13.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.838][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:13.839][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:13.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.840][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.842][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:13.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:13.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.846][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:13.847][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:13.848][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.848][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.850][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:13.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:13.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.854][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:13.855][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:13.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.857][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.858][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:13.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:13.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.863][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:13.864][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:13.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.867][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.868][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:13.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:13.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.873][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:13.874][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:13.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.877][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.878][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:13.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:13.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.883][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:13.885][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:13.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.886][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.887][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:13.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:13.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.891][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:13.892][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:13.893][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.894][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.896][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:13.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:13.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.902][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:13.903][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:13.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.905][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.906][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:13.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:13.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.910][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:13.911][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:13.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.913][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.915][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:13.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:13.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.919][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:13.920][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:13.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.922][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.923][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:13.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:13.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:13.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:13.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:13.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:13.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:13.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:13.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.940][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:13.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:13.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:13.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:13.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:13.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:13.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:13.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:13.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:13.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:13.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:13.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:13.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:13.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:13.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:13.973][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-03-19 19:45:13.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:13.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:13.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:13.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:13.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:13.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:13.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:13.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:13.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:13.988][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:13.989][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:13.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:13.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:13.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:14.000][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:14.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:14.002][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:14.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:14.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.007][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:14.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:14.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:14.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:14.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:14.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:14.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:14.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:14.027][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:14.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:14.029][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:14.030][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.DEBUG[2025-03-19 19:45:14.031][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-03-19 19:45:14.032][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:45:14.033][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-03-19 19:45:14.034][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:45:14.035][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:45:14.036][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:45:14.037][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:45:14.038][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:45:14.040][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:45:14.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:14.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:14.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:14.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:14.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:14.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:14.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:14.057][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-03-19 19:45:14.060][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:14.061][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:14.063][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-03-19 19:45:14.424][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-03-19 19:45:14.792][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2025-03-19 19:45:14.794][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-03-19 19:45:14.796][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-03-19 19:45:14.800][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-03-19 19:45:14.803][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-03-19 19:45:14.805][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:45:14.807][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:45:14.808][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:45:14.810][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:14.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:14.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:14.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:14.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:14.823][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:14.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:14.827][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:14.829][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:14.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.831][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:14.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:14.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.836][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:14.837][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:14.838][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.839][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.841][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:14.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:14.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.846][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:14.847][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:14.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.848][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.850][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:14.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:14.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.856][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:14.857][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:14.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.859][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.860][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:14.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:14.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.865][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:14.866][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:14.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.869][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.870][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:14.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:14.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.893][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:14.895][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:14.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.896][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.898][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:14.899][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:14.900][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.902][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.903][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:14.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:14.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.908][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:14.909][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:14.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.911][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:14.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:14.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.918][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:14.919][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:14.919][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.920][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.921][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:14.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:14.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.925][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:14.926][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:14.927][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.928][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.930][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:14.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:14.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.934][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:14.935][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:14.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.938][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.939][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:14.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:14.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:14.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:14.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:14.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:14.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:14.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:14.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:14.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:14.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:14.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:14.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:14.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:14.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:14.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:14.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:14.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:14.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:14.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:14.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:14.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:14.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:14.987][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-03-19 19:45:14.989][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:14.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:14.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:14.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:14.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:14.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:14.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:14.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:14.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:15.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:15.026][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:15.030][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:15.031][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:15.034][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-19 19:45:15.626][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-19 19:45:16.135][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:16.137][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-03-19 19:45:16.142][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-03-19 19:45:16.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.156][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.172][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.195][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.207][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.214][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.215][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.230][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.239][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.240][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.271][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.272][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.282][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.296][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.297][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.305][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.342][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.351][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.352][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.378][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.387][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.413][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.424][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.TRACE[2025-03-19 19:45:16.425][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.432][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.436][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.445][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.446][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.TRACE[2025-03-19 19:45:16.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.459][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.459][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.469][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.470][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.481][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.482][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.489][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.491][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.492][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.TRACE[2025-03-19 19:45:16.493][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.504][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.505][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.541][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.543][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.557][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.567][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.569][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.591][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.592][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.TRACE[2025-03-19 19:45:16.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.619][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.620][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[2025-03-19 19:45:16.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.645][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.647][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.654][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.658][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.663][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.674][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.714][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:16.719][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:45:16.721][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-19 19:45:16.722][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:45:16.724][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-19 19:45:16.727][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.737][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.744][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.750][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.764][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.790][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.791][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.800][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.802][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.803][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[2025-03-19 19:45:16.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.834][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.836][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.879][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.880][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.TRACE[2025-03-19 19:45:16.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.903][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.925][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.927][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.947][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.951][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.966][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:16.968][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:16.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:16.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:16.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:16.978][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:16.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:16.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.986][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:16.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:16.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:16.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:16.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:17.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:17.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:17.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:17.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:17.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:17.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:17.016][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:17.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:17.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:17.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:17.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:17.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:17.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:17.040][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.TRACE[2025-03-19 19:45:17.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:17.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:17.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:17.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:17.063][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:17.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:17.065][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:17.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:17.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:17.080][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:17.081][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:17.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:17.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:17.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:17.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:17.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:17.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:17.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:17.108][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:17.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:17.115][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:17.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:17.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:17.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:17.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:17.131][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:17.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:17.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:17.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:17.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:17.143][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:17.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:17.145][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:17.157][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:17.159][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:17.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:17.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:17.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:17.169][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:17.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:17.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:17.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:17.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:17.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:17.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:17.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:17.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:17.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:17.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:17.211][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:17.212][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:17.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:17.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:17.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:17.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:17.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:17.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.229][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:17.236][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:17.237][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:17.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:17.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:17.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:17.245][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:17.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:17.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:17.264][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:17.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:17.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:17.272][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:17.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:17.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:17.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:17.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:17.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.307][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-19 19:45:17.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-19 19:45:17.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-19 19:45:17.320][biodb::testThat]
biodb.INFO [2025-03-19 19:45:17.321][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-03-19 19:45:17.322][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:45:17.322][biodb::testThat]
biodb.TRACE[2025-03-19 19:45:17.325][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-19 19:45:17.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-19 19:45:17.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:17.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:17.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.332][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:17.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:17.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.335][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:17.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:17.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:17.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:17.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:17.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:17.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:17.344][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:17.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:17.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:17.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:17.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:17.352][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:17.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:17.356][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:17.358][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:17.359][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:17.361][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-19 19:45:17.715][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-19 19:45:18.107][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2025-03-19 19:45:18.109][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-03-19 19:45:18.111][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-03-19 19:45:18.116][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-03-19 19:45:18.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:18.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:18.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:18.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:18.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:18.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:18.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:18.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:18.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:18.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:18.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:18.137][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:18.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:18.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:18.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:18.141][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:18.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:18.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:18.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:18.146][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:18.149][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:18.150][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:18.151][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-19 19:45:18.520][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-19 19:45:18.882][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:18.885][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-03-19 19:45:18.889][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-03-19 19:45:18.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:18.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:18.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:18.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:18.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:18.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:18.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:18.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:18.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:18.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:18.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:18.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:18.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:18.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:18.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:18.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:18.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:18.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:18.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:18.919][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:18.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:18.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:18.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:18.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:18.929][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:18.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:18.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:18.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:18.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:18.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:18.935][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:18.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:18.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:18.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:18.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:18.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:18.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:18.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:18.943][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-19 19:45:18.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:18.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:18.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:18.952][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:18.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:18.954][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:18.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:18.956][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:18.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:18.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:18.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:18.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:18.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:18.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:18.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:18.964][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:18.965][private$selectFields]
biodb.TRACE[2025-03-19 19:45:18.966][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 19:45:18.967][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 19:45:18.968][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:18.969][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:18.970][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:18.971][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:18.972][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:18.973][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:18.975][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:18.976][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:18.977][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:18.978][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:18.979][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:18.980][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:18.981][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:18.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:18.982][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:18.983][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 19:45:18.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:18.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:18.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:18.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:18.989][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:18.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:18.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:18.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:18.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:18.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:18.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:18.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:19.008][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-19 19:45:19.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:19.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:19.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:19.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:19.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:19.019][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:19.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:19.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:19.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:19.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:19.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:19.028][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:19.029][private$selectFields]
biodb.TRACE[2025-03-19 19:45:19.030][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 19:45:19.031][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 19:45:19.032][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:19.032][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.033][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:19.035][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:19.036][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.037][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:19.038][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:19.040][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:19.041][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:19.042][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.043][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:19.045][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:19.046][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 19:45:19.047][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:19.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:19.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:19.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:19.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:19.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:19.060][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-19 19:45:19.062][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:19.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:19.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:19.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:19.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:19.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:19.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:19.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:19.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:19.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:19.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:19.082][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:19.083][private$selectFields]
biodb.TRACE[2025-03-19 19:45:19.084][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 19:45:19.085][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 19:45:19.086][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:19.087][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.088][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.089][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:19.090][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:19.091][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.092][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:19.094][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:19.095][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:19.096][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:19.098][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.099][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:19.101][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:19.115][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 19:45:19.116][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:19.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:19.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:19.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:19.125][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:19.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:19.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:19.129][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-19 19:45:19.131][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-19 19:45:19.132][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-19 19:45:19.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:19.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:19.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:19.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:19.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:19.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:19.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:19.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:19.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:19.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:19.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:19.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:19.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:19.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:19.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:19.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:19.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:19.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:19.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:19.228][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:19.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:19.231][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:19.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:19.234][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:19.237][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:19.238][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:19.240][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-19 19:45:20.592][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-19 19:45:20.960][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:20.962][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-03-19 19:45:20.967][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-03-19 19:45:20.971][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:20.974][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:20.975][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:20.977][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-19 19:45:21.340][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-19 19:45:22.113][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:22.116][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-03-19 19:45:22.120][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-03-19 19:45:22.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:22.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:22.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:22.132][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:22.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:22.134][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:22.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:22.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:22.152][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:22.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:22.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:22.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:22.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:22.163][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:22.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:22.165][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:22.178][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:22.179][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:22.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:22.186][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:22.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:22.188][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:22.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:22.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:22.227][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-19 19:45:22.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:22.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:22.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:22.263][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:22.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:22.265][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:22.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:22.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.276][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.278][private$selectFields]
biodb.TRACE[2025-03-19 19:45:22.279][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 19:45:22.279][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 19:45:22.280][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.281][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.282][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.283][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.284][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.285][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.286][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.287][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.288][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.289][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.290][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.291][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.293][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.294][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 19:45:22.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.308][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-19 19:45:22.309][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:22.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:22.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:22.319][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:22.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:22.321][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:22.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:22.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.357][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.382][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.383][private$selectFields]
biodb.TRACE[2025-03-19 19:45:22.385][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 19:45:22.386][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 19:45:22.387][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.388][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.389][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.391][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.392][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.393][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.395][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.396][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.407][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.408][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.409][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.411][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.412][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 19:45:22.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.426][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-19 19:45:22.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:22.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:22.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:22.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:22.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:22.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:22.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:22.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.445][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.446][private$selectFields]
biodb.TRACE[2025-03-19 19:45:22.447][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 19:45:22.448][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 19:45:22.448][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.450][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.451][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.452][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.453][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.455][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.455][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.457][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.458][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.459][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.460][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.461][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.463][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.465][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 19:45:22.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.479][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-19 19:45:22.481][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-19 19:45:22.482][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-19 19:45:22.493][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-19 19:45:22.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-19 19:45:22.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-19 19:45:22.502][biodb::testThat]
biodb.INFO [2025-03-19 19:45:22.503][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-03-19 19:45:22.505][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:45:22.506][biodb::testThat]
biodb.TRACE[2025-03-19 19:45:22.510][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-19 19:45:22.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-19 19:45:22.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.524][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:22.537][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:22.537][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:22.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:22.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:22.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:22.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:22.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:22.549][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:22.552][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:45:22.554][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-19 19:45:22.555][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:45:22.557][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-19 19:45:22.560][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:22.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:22.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:22.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:22.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:22.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:22.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:22.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.577][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.582][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:22.587][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:22.590][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:45:22.591][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-19 19:45:22.593][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:45:22.594][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-19 19:45:22.597][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:22.598][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:22.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:22.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:22.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:22.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:22.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:22.610][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.618][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:22.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:22.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:22.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:22.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:22.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:22.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:22.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:22.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:22.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:22.649][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-19 19:45:22.651][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:22.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:22.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:22.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:22.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:22.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:22.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:22.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.667][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.671][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.672][private$selectFields]
biodb.TRACE[2025-03-19 19:45:22.673][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 19:45:22.674][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 19:45:22.675][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.676][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.677][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.678][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.679][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.679][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.681][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.683][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.684][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.685][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.686][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.688][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.690][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.690][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 19:45:22.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.696][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.700][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.704][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-19 19:45:22.705][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:22.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:22.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:22.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:22.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:22.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:22.717][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.TRACE[2025-03-19 19:45:22.719][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.730][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.733][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.734][private$selectFields]
biodb.TRACE[2025-03-19 19:45:22.735][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 19:45:22.736][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 19:45:22.737][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.738][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.739][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.740][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.741][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.741][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.743][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.744][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.745][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.746][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.747][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.748][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.750][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.751][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 19:45:22.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.760][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.764][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-19 19:45:22.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:22.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:22.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:22.773][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:22.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:22.775][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:22.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:22.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.781][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.786][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.787][private$selectFields]
biodb.TRACE[2025-03-19 19:45:22.788][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 19:45:22.788][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 19:45:22.789][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.790][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.791][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.792][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.793][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.794][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.795][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.796][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.797][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.798][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.799][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.800][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.801][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.803][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.804][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 19:45:22.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.818][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-19 19:45:22.819][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-19 19:45:22.820][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-19 19:45:22.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:22.852][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:22.852][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:22.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:22.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:22.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:22.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:22.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:22.865][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:22.868][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:45:22.869][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-19 19:45:22.870][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:45:22.871][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-19 19:45:22.874][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:22.877][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:45:22.878][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-19 19:45:22.879][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:45:22.880][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-19 19:45:22.884][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:22.885][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:22.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:22.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:22.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:22.895][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:22.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:22.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.902][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:22.910][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:22.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:22.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:22.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:22.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:22.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:22.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:22.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.929][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:22.938][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:22.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:22.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:22.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:22.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:22.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:22.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:22.951][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.954][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:22.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:22.961][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-19 19:45:22.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:22.963][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:22.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:22.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:22.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:22.973][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:22.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:22.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.984][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.985][private$selectFields]
biodb.TRACE[2025-03-19 19:45:22.986][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 19:45:22.987][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 19:45:22.987][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.989][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.990][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.992][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.993][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.994][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:22.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:22.996][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:22.997][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:22.998][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.000][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.001][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.002][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.003][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 19:45:23.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.017][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-19 19:45:23.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:23.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:23.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:23.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:23.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:23.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:23.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:23.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.040][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.041][private$selectFields]
biodb.TRACE[2025-03-19 19:45:23.042][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 19:45:23.043][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 19:45:23.044][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.046][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.047][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.049][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.050][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.051][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.053][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.054][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.055][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.056][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.057][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.059][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.060][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 19:45:23.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.074][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-19 19:45:23.075][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:23.076][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:23.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:23.084][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:23.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:23.086][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:23.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:23.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.093][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.097][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.099][private$selectFields]
biodb.TRACE[2025-03-19 19:45:23.100][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 19:45:23.101][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 19:45:23.102][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.104][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.105][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.108][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.109][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.110][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.111][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.112][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.113][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.114][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.123][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.124][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.127][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.128][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 19:45:23.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.137][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.142][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-19 19:45:23.143][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-19 19:45:23.144][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-19 19:45:23.155][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-19 19:45:23.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-19 19:45:23.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-19 19:45:23.164][biodb::testThat]
biodb.INFO [2025-03-19 19:45:23.166][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-03-19 19:45:23.167][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:45:23.168][biodb::testThat]
biodb.TRACE[2025-03-19 19:45:23.172][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-19 19:45:23.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-19 19:45:23.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.182][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.186][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.190][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:23.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:23.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:23.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:23.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:23.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:23.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:23.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:23.213][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:23.217][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:45:23.218][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-19 19:45:23.220][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:45:23.221][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-19 19:45:23.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:23.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:23.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:23.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:23.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:23.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:23.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:23.237][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:23.251][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:23.254][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:45:23.255][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-19 19:45:23.257][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:45:23.259][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-19 19:45:23.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:23.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:23.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:23.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:23.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:23.273][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:23.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:23.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:23.288][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:23.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:23.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:23.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:23.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:23.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:23.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:23.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.306][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.312][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:23.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:23.316][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-19 19:45:23.318][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:23.319][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:23.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:23.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:23.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:23.330][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:23.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:23.332][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.340][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.341][private$selectFields]
biodb.TRACE[2025-03-19 19:45:23.342][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 19:45:23.343][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 19:45:23.344][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.345][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.347][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.348][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.349][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.350][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.352][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.354][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.356][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.357][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.358][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.360][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.362][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.364][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 19:45:23.365][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.379][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-19 19:45:23.380][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:23.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:23.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:23.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:23.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:23.392][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:23.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:23.395][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.404][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.405][private$selectFields]
biodb.TRACE[2025-03-19 19:45:23.406][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 19:45:23.407][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 19:45:23.408][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.409][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.411][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.411][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.412][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.414][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.415][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.416][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.417][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.419][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.420][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.421][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.422][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.423][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.424][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 19:45:23.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.435][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.440][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-19 19:45:23.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:23.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:23.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:23.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:23.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:23.452][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:23.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:23.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.464][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.465][private$selectFields]
biodb.TRACE[2025-03-19 19:45:23.466][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 19:45:23.468][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 19:45:23.469][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.470][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.471][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.473][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.474][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.475][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.476][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.477][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.477][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.478][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.479][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.480][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.481][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.482][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.483][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 19:45:23.485][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.499][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-19 19:45:23.500][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-19 19:45:23.501][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-19 19:45:23.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:23.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:23.560][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:23.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:23.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:23.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:23.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:23.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:23.576][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:23.579][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:45:23.581][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-19 19:45:23.582][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:45:23.584][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-19 19:45:23.588][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:23.593][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:45:23.595][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-19 19:45:23.602][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:45:23.604][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-19 19:45:23.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:23.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:23.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:23.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:23.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:23.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:23.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:23.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.625][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:23.632][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:23.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:23.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:23.639][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:23.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:23.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:23.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:23.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:23.653][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:23.654][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:23.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:23.661][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:23.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:23.663][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:23.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:23.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.674][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:23.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:23.677][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-19 19:45:23.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:23.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:23.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:23.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:23.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:23.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:23.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:23.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.701][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.702][private$selectFields]
biodb.TRACE[2025-03-19 19:45:23.703][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 19:45:23.704][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 19:45:23.706][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.707][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.708][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.710][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.711][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.712][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.713][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.714][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.715][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.716][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.717][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.718][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.719][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 19:45:23.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.727][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.731][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-19 19:45:23.732][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:23.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:23.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:23.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:23.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:23.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:23.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:23.742][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.751][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.752][private$selectFields]
biodb.TRACE[2025-03-19 19:45:23.753][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 19:45:23.754][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 19:45:23.755][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.756][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.757][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.758][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.759][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.760][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.762][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.763][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.764][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.765][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.766][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.767][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.768][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.769][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 19:45:23.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.774][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.778][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.784][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-19 19:45:23.786][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:23.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:23.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:23.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:23.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:23.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:23.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:23.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.802][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.806][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.807][private$selectFields]
biodb.TRACE[2025-03-19 19:45:23.808][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 19:45:23.810][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 19:45:23.811][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.811][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.812][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.813][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.814][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.815][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.816][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.818][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.819][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.820][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 19:45:23.821][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.822][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.824][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.825][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 19:45:23.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:23.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:23.842][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-19 19:45:23.843][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-19 19:45:23.844][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-19 19:45:23.870][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-19 19:45:23.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-19 19:45:23.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:23.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-19 19:45:23.879][biodb::testThat]
biodb.INFO [2025-03-19 19:45:23.880][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-03-19 19:45:23.882][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:45:23.883][biodb::testThat]
biodb.DEBUG[2025-03-19 19:45:23.885][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-03-19 19:45:23.886][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:45:23.887][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-03-19 19:45:23.889][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:45:23.891][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:45:23.892][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:45:23.893][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:45:23.894][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:45:23.895][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:45:23.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:23.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:23.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:23.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:23.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:23.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:23.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:23.912][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-03-19 19:45:23.915][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:23.916][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:23.917][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-03-19 19:45:24.275][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-03-19 19:45:24.637][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:24.640][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-03-19 19:45:24.645][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-03-19 19:45:24.649][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-03-19 19:45:24.651][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:45:24.653][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:45:24.654][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:45:24.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:24.656][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:24.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:24.665][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:24.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:24.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:24.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:24.671][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:24.672][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:24.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.674][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:24.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:24.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:24.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:24.679][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:24.680][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:24.694][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.695][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:24.697][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:24.698][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:24.699][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.700][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:24.702][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:24.703][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:24.704][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.705][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:24.706][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:24.707][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:24.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.709][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:24.710][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:24.711][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:24.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.713][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:24.714][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:24.715][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:24.716][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.717][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:24.718][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:24.719][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:24.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.720][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:24.722][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:24.723][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:24.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.726][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:24.728][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:24.729][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:24.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.731][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:24.733][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:24.734][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:24.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.736][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:24.737][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:24.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:24.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:24.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:24.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:24.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:24.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:24.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:24.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:24.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:24.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:24.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:24.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:24.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:24.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:24.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:24.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:24.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:24.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:24.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:24.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:24.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:24.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:24.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:24.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:24.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:24.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:24.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:24.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:24.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:24.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:24.775][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-03-19 19:45:24.777][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-03-19 19:45:24.787][biodb::testThat]
biodb.INFO [2025-03-19 19:45:24.788][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-03-19 19:45:24.790][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:45:24.790][biodb::testThat]
biodb.DEBUG[2025-03-19 19:45:24.800][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-03-19 19:45:24.802][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-03-19 19:45:24.803][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-03-19 19:45:24.806][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-03-19 19:45:24.808][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-03-19 19:45:24.809][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:45:24.811][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:45:24.812][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:45:24.814][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:45:24.815][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:45:24.818][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:24.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:24.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:24.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:24.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:24.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:24.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:24.833][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-03-19 19:45:24.836][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:24.836][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:24.838][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-03-19 19:45:25.197][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-03-19 19:45:25.556][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:25.560][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-03-19 19:45:25.564][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-03-19 19:45:25.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:25.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:25.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:25.577][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:25.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:25.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:25.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:25.581][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-03-19 19:45:25.584][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:25.585][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:25.587][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-03-19 19:45:25.954][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-03-19 19:45:26.811][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:26.816][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-03-19 19:45:26.820][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-03-19 19:45:26.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:26.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:26.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:26.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:26.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:26.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:26.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:26.837][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-03-19 19:45:26.840][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:26.842][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:26.843][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-03-19 19:45:27.212][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-03-19 19:45:27.584][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:27.586][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-03-19 19:45:27.590][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-03-19 19:45:27.593][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-03-19 19:45:27.595][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:45:27.596][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-03-19 19:45:27.597][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-03-19 19:45:27.599][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:27.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:27.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:27.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:27.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:27.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:27.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:27.614][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:27.615][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:27.617][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.618][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:27.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:27.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.624][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:27.625][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:27.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.627][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.629][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:27.630][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:27.630][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.631][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.633][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:27.634][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:27.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.636][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.637][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:27.639][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:27.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.641][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.642][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:27.643][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:27.644][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.645][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.646][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:27.648][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:27.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.650][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.651][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:27.653][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:27.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.655][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.656][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:27.657][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:27.658][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.659][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.661][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:27.662][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:27.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.665][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.666][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:27.668][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:27.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.670][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:27.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:27.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.676][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:27.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:27.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:27.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:27.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.686][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:27.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:27.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:27.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:27.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:27.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:27.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:27.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:27.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:27.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:27.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:27.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:27.718][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:27.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:27.721][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:27.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:27.725][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:27.727][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:27.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.729][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:27.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:27.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.736][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:27.738][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:27.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.740][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.742][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:27.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:27.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.747][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:27.748][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:27.750][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.751][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.753][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:27.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:27.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.759][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:27.760][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:27.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.763][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.764][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:27.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:27.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.770][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:27.772][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:27.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.774][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.775][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:27.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:27.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.779][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:27.780][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:27.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.782][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.783][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:27.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:27.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.786][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:27.787][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:27.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.789][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.808][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:27.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:27.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.814][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:27.816][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:27.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.818][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.820][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:27.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:27.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.825][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:27.826][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:27.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.828][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.830][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:27.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:27.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.835][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:27.836][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:27.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.839][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.840][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:27.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:27.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.845][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:27.846][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:27.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.848][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.850][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:27.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:27.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:27.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:27.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:27.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:27.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:27.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:27.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:27.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:27.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:27.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:27.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:27.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:27.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:27.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:27.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:27.886][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:27.887][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:27.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:27.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:27.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:27.895][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:27.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:27.899][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:27.900][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:27.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.903][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:27.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:27.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.908][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:27.909][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:27.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.912][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.913][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:27.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:27.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.918][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:27.919][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:27.920][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.921][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.922][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:27.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:27.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.926][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:27.927][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:27.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.929][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.931][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:27.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:27.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.935][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:27.937][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:27.938][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.939][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.940][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:27.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:27.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.945][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:27.946][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:27.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.947][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.948][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:27.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:27.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.954][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:27.955][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:27.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.958][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.959][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:27.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:27.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.965][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:27.967][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:27.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.969][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.971][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:27.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:27.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.977][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:27.978][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:27.979][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.980][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.982][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:27.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:27.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.988][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:27.989][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:27.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.991][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.993][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:27.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:27.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:27.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:27.997][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:27.998][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:27.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:28.000][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:28.001][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:28.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:28.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:28.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:28.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:28.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:28.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:28.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:28.010][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:28.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:28.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:28.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:28.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:28.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:28.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:28.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:28.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:28.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:28.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:28.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:28.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:28.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:28.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:28.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:28.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:28.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:28.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:28.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:28.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:28.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:28.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:28.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:28.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:28.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:28.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:28.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:28.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:28.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:28.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:28.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:28.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:28.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:28.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:28.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:28.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:28.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:28.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:28.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:28.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:28.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:28.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:28.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:28.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:28.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:28.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:28.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:28.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:28.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:28.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:28.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:28.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:28.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:28.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:28.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:28.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:28.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:28.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:28.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:28.070][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-03-19 19:45:28.071][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-03-19 19:45:28.072][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-03-19 19:45:28.090][biodb::testThat]
biodb.INFO [2025-03-19 19:45:28.091][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-03-19 19:45:28.092][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:45:28.093][biodb::testThat]
biodb.INFO [2025-03-19 19:45:28.122][biodb::testThat]
biodb.INFO [2025-03-19 19:45:28.123][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-03-19 19:45:28.124][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:45:28.125][biodb::testThat]
biodb.INFO [2025-03-19 19:45:28.137][biodb::testThat]
biodb.INFO [2025-03-19 19:45:28.138][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-03-19 19:45:28.140][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:45:28.140][biodb::testThat]
biodb.DEBUG[2025-03-19 19:45:28.144][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:28.148][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:28.149][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:28.152][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-03-19 19:45:28.580][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-03-19 19:45:29.136][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:29.138][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-03-19 19:45:29.142][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-03-19 19:45:29.157][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:29.159][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:29.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:29.160][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:29.161][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:29.162][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:29.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:29.165][ef$get] fields variable is a list.
biodb.INFO [2025-03-19 19:45:29.167][biodb::testThat]
biodb.INFO [2025-03-19 19:45:29.168][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2025-03-19 19:45:29.169][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:45:29.169][biodb::testThat]
biodb.ERROR[2025-03-19 19:45:29.187][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-03-19 19:45:29.215][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-03-19 19:45:29.231][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-19 19:45:29.233][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-19 19:45:29.235][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-19 19:45:29.235][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-19 19:45:29.236][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:29.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:29.238][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.240][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-19 19:45:29.254][biodb::testContext]
biodb.INFO [2025-03-19 19:45:29.255][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-19 19:45:29.256][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-03-19 19:45:29.257][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-19 19:45:29.258][biodb::testContext]
biodb.INFO [2025-03-19 19:45:29.260][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-19 19:45:29.262][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-19 19:45:29.266][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 19:45:29.267][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-19 19:45:29.269][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-19 19:45:29.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.272][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-19 19:45:29.273][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-19 19:45:29.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.277][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-19 19:45:29.278][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-19 19:45:29.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.281][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-19 19:45:29.282][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-19 19:45:29.283][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-19 19:45:29.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.286][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-19 19:45:29.287][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-19 19:45:29.288][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-19 19:45:29.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.292][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-19 19:45:29.293][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-19 19:45:29.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.297][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-19 19:45:29.298][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-19 19:45:29.299][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-19 19:45:29.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.302][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-19 19:45:29.303][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-19 19:45:29.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.307][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-19 19:45:29.308][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-19 19:45:29.309][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-19 19:45:29.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.313][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-19 19:45:29.314][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-19 19:45:29.315][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-19 19:45:29.316][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-19 19:45:29.317][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-19 19:45:29.318][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-19 19:45:29.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.322][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-19 19:45:29.324][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-19 19:45:29.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.328][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-19 19:45:29.329][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-19 19:45:29.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.332][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.DEBUG[2025-03-19 19:45:29.333][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-19 19:45:29.334][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-19 19:45:29.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.338][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-19 19:45:29.339][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-19 19:45:29.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.343][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-19 19:45:29.345][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-19 19:45:29.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.349][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-19 19:45:29.350][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-19 19:45:29.371][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-19 19:45:29.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.376][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-19 19:45:29.377][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-19 19:45:29.378][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-19 19:45:29.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.382][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-19 19:45:29.384][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:29.385][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-19 19:45:29.385][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:29.386][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 19:45:29.387][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:29.388][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 19:45:29.389][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:29.390][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 19:45:29.391][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-19 19:45:29.391][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 19:45:29.392][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:29.393][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-19 19:45:29.394][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 19:45:29.395][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:29.396][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:29.397][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 19:45:29.397][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 19:45:29.397][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 19:45:29.397][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-19 19:45:29.397][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-19 19:45:29.397][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 19:45:29.398][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:29.399][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:29.400][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 19:45:29.401][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:29.402][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:29.403][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 19:45:29.404][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:29.405][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 19:45:29.405][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 19:45:29.406][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:29.407][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:29.409][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-19 19:45:29.411][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:29.412][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-19 19:45:29.413][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:29.414][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 19:45:29.414][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:29.415][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 19:45:29.416][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:29.418][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 19:45:29.419][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-19 19:45:29.420][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 19:45:29.421][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:29.422][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-19 19:45:29.423][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 19:45:29.424][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:29.425][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:29.426][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 19:45:29.426][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 19:45:29.426][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 19:45:29.426][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-19 19:45:29.426][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-19 19:45:29.427][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 19:45:29.428][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:29.429][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:29.430][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 19:45:29.431][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:29.432][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:29.433][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 19:45:29.434][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:29.435][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 19:45:29.436][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 19:45:29.437][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:29.438][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:29.439][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-19 19:45:29.441][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:29.442][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-19 19:45:29.443][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:29.444][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 19:45:29.445][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:29.446][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 19:45:29.447][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:29.448][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 19:45:29.449][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-19 19:45:29.450][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 19:45:29.451][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:29.452][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-19 19:45:29.452][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 19:45:29.454][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:29.455][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:29.456][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:29.457][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 19:45:29.458][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:29.459][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:29.460][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 19:45:29.461][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:29.461][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:29.462][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 19:45:29.463][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:29.464][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 19:45:29.465][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 19:45:29.465][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:29.466][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:29.468][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-19 19:45:29.470][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:29.471][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-19 19:45:29.472][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:29.473][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 19:45:29.473][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:29.474][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 19:45:29.475][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:29.476][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 19:45:29.477][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-19 19:45:29.478][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 19:45:29.479][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:29.479][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-19 19:45:29.480][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 19:45:29.481][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:29.482][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:29.483][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:29.484][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 19:45:29.485][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:29.485][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:29.486][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 19:45:29.487][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:29.488][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:29.489][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 19:45:29.490][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:29.491][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 19:45:29.491][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 19:45:29.492][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:29.493][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:29.495][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 19:45:29.496][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.507][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.DEBUG[2025-03-19 19:45:29.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.511][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[2025-03-19 19:45:29.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.531][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[2025-03-19 19:45:29.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.584][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-19 19:45:29.586][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-19 19:45:29.588][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-19 19:45:29.590][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-19 19:45:29.591][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-19 19:45:29.592][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-19 19:45:29.593][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-19 19:45:29.595][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-19 19:45:29.596][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-19 19:45:29.597][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-19 19:45:29.598][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-19 19:45:29.600][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-19 19:45:29.601][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-19 19:45:29.603][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-19 19:45:29.605][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-19 19:45:29.606][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-19 19:45:29.607][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-19 19:45:29.608][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-19 19:45:29.609][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-19 19:45:29.611][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-19 19:45:29.612][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-19 19:45:29.613][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-19 19:45:29.614][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-19 19:45:29.615][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-19 19:45:29.617][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-19 19:45:29.618][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-19 19:45:29.619][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-19 19:45:29.620][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-19 19:45:29.621][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-19 19:45:29.622][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-19 19:45:29.624][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-19 19:45:29.625][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-19 19:45:29.626][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-19 19:45:29.627][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-19 19:45:29.628][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-19 19:45:29.630][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-19 19:45:29.631][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-19 19:45:29.633][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-19 19:45:29.634][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-19 19:45:29.636][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-19 19:45:29.637][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-19 19:45:29.639][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-19 19:45:29.640][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-19 19:45:29.641][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-19 19:45:29.642][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-19 19:45:29.643][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-19 19:45:29.644][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-19 19:45:29.646][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-19 19:45:29.647][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-19 19:45:29.648][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-19 19:45:29.649][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-19 19:45:29.650][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-19 19:45:29.651][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-19 19:45:29.653][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-19 19:45:29.654][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-19 19:45:29.655][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-19 19:45:29.656][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-19 19:45:29.658][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-19 19:45:29.659][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-19 19:45:29.660][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-19 19:45:29.661][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-19 19:45:29.663][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-19 19:45:29.664][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-19 19:45:29.665][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-19 19:45:29.666][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-19 19:45:29.668][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-19 19:45:29.669][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-19 19:45:29.670][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-19 19:45:29.671][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-19 19:45:29.674][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-19 19:45:29.675][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-19 19:45:29.677][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-19 19:45:29.678][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-19 19:45:29.679][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-19 19:45:29.680][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-19 19:45:29.681][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-19 19:45:29.683][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-19 19:45:29.684][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-19 19:45:29.685][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-19 19:45:29.686][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-19 19:45:29.688][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-19 19:45:29.689][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-19 19:45:29.691][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-19 19:45:29.692][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-19 19:45:29.694][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-19 19:45:29.695][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 19:45:29.697][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.698][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:29.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:29.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:29.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:29.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:29.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:29.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:29.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:29.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:29.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:29.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:29.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:29.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:29.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:29.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:29.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:29.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:29.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:29.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:29.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:29.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:29.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:29.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:29.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:29.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:29.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:29.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:29.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:29.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:29.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:29.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:29.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:29.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:29.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:29.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:29.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:29.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:29.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:29.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:29.811][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-19 19:45:29.813][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-19 19:45:29.815][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:29.816][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-19 19:45:29.817][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:29.817][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 19:45:29.819][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:29.820][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 19:45:29.821][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:29.822][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-19 19:45:29.824][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-19 19:45:29.825][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 19:45:29.826][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:29.827][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-19 19:45:29.829][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 19:45:29.830][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-19 19:45:29.830][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-19 19:45:29.830][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-19 19:45:29.830][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-19 19:45:29.830][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-19 19:45:29.830][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-19 19:45:29.830][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-19 19:45:29.830][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-19 19:45:29.830][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-19 19:45:29.830][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-19 19:45:29.830][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-19 19:45:29.831][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:29.832][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 19:45:29.832][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 19:45:29.832][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 19:45:29.833][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-19 19:45:29.834][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:29.835][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:29.836][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 19:45:29.837][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:29.838][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:29.839][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 19:45:29.840][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:45:29.840][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-19 19:45:29.841][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 19:45:29.842][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 19:45:29.843][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:29.845][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-19 19:45:29.845][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-19 19:45:29.847][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-19 19:45:29.849][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-19 19:45:29.850][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-19 19:45:29.852][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-19 19:45:29.854][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-19 19:45:29.856][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-19 19:45:29.860][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-19 19:45:29.861][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-19 19:45:29.862][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-19 19:45:29.864][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-19 19:45:29.865][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-19 19:45:29.866][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-19 19:45:29.868][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-19 19:45:29.869][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-19 19:45:29.870][biodb::testThat]
biodb.INFO [2025-03-19 19:45:29.871][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2025-03-19 19:45:29.872][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:45:29.873][biodb::testThat]
biodb.DEBUG[2025-03-19 19:45:29.877][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-19 19:45:29.882][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:29.883][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:29.885][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-03-19 19:45:30.243][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-03-19 19:45:30.742][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:30.745][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-03-19 19:45:30.750][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-03-19 19:45:30.756][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:30.759][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:30.760][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:30.762][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-19 19:45:31.144][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-19 19:45:31.510][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:31.513][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-03-19 19:45:31.519][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-03-19 19:45:31.521][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:31.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:31.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:31.531][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:31.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:31.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:31.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:31.536][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:31.555][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:31.557][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:31.559][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-19 19:45:31.916][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-19 19:45:32.276][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:32.279][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-03-19 19:45:32.284][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-03-19 19:45:32.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:32.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:32.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:32.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:32.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:32.300][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:32.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:32.325][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:32.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:32.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:32.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:32.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:32.337][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:32.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:32.345][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:32.349][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:45:32.351][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-19 19:45:32.353][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:45:32.355][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-19 19:45:32.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:32.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:32.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:32.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:32.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:32.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:32.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:32.373][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:32.378][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:45:32.380][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-19 19:45:32.381][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:45:32.383][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-19 19:45:32.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:32.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:32.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:32.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:32.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:32.399][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:32.400][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.DEBUG[2025-03-19 19:45:32.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:32.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:32.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:32.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:32.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:32.412][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:32.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:32.419][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:32.423][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:45:32.425][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-19 19:45:32.426][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:45:32.428][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-19 19:45:32.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:32.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:32.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:32.439][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:32.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:32.442][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:32.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:32.446][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:32.450][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:45:32.452][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-19 19:45:32.454][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:45:32.456][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-19 19:45:32.458][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:32.459][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:32.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:32.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:32.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:32.470][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:32.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:32.474][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:32.479][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:32.480][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:32.483][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-19 19:45:32.857][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-19 19:45:33.223][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:33.225][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-03-19 19:45:33.230][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-03-19 19:45:33.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:33.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:33.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:33.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:33.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:33.245][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:33.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-19 19:45:33.256][biodb::testThat]
biodb.INFO [2025-03-19 19:45:33.257][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2025-03-19 19:45:33.258][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:45:33.260][biodb::testThat]
biodb.DEBUG[2025-03-19 19:45:33.264][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:33.269][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:33.271][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:33.274][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-19 19:45:33.638][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-19 19:45:34.000][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:34.002][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-03-19 19:45:34.009][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-03-19 19:45:34.012][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:34.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:34.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:34.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:34.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:34.024][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:34.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:34.032][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:34.036][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:34.038][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:34.041][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-19 19:45:34.405][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-19 19:45:34.766][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:34.769][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-03-19 19:45:34.775][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-03-19 19:45:34.778][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:34.779][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:34.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:34.785][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:34.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:34.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:34.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-19 19:45:34.796][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-19 19:45:34.797][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-19 19:45:34.798][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-19 19:45:34.799][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-19 19:45:34.800][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:34.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:34.803][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:34.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:34.805][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:34.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-19 19:45:34.810][biodb::testContext]
biodb.INFO [2025-03-19 19:45:34.811][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-19 19:45:34.813][biodb::testContext] Test context - Test web services
biodb.INFO [2025-03-19 19:45:34.814][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-19 19:45:34.815][biodb::testContext]
biodb.INFO [2025-03-19 19:45:34.819][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-19 19:45:34.821][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-19 19:45:34.827][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 19:45:34.828][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-19 19:45:34.830][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-19 19:45:34.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:34.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:34.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:34.833][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-19 19:45:34.834][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-19 19:45:34.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:34.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:34.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:34.838][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-19 19:45:34.839][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-19 19:45:34.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:34.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:34.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:34.844][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-19 19:45:34.845][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-19 19:45:34.847][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-19 19:45:34.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:34.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:34.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:34.851][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-19 19:45:34.853][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-19 19:45:34.854][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-19 19:45:34.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:34.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:34.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:34.859][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-19 19:45:34.860][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-19 19:45:34.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:34.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:34.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:34.865][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-19 19:45:34.866][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-19 19:45:34.868][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-19 19:45:34.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:34.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:34.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:34.873][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-19 19:45:34.874][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-19 19:45:34.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:34.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:34.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:34.878][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-19 19:45:34.879][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-19 19:45:34.881][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-19 19:45:34.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:34.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:34.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:34.884][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-19 19:45:34.885][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-19 19:45:34.886][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-19 19:45:34.887][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-19 19:45:34.888][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-19 19:45:34.889][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-19 19:45:34.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:34.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:34.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:34.894][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-19 19:45:34.896][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-19 19:45:34.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:34.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:34.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:34.900][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-19 19:45:34.901][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-19 19:45:34.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:34.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:34.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:34.906][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-19 19:45:34.907][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-19 19:45:34.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:34.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:34.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:34.911][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-19 19:45:34.913][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-19 19:45:34.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:34.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:34.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:34.916][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-19 19:45:34.917][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-19 19:45:34.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:34.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:34.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:34.941][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-19 19:45:34.943][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-19 19:45:34.985][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-19 19:45:34.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:34.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:34.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:34.990][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-19 19:45:34.991][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-19 19:45:34.992][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-19 19:45:34.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:34.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:34.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:34.997][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-19 19:45:34.999][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:35.000][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-19 19:45:35.001][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:35.002][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 19:45:35.003][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:35.004][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 19:45:35.005][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:35.006][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 19:45:35.007][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-19 19:45:35.008][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 19:45:35.009][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:35.011][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-19 19:45:35.011][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 19:45:35.012][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:35.013][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:35.014][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 19:45:35.014][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 19:45:35.014][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 19:45:35.014][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-19 19:45:35.014][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-19 19:45:35.015][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 19:45:35.016][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:35.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:35.017][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 19:45:35.018][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:35.019][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:35.021][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 19:45:35.022][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:35.023][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 19:45:35.024][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 19:45:35.025][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:35.026][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:35.027][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-19 19:45:35.028][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:35.029][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-19 19:45:35.030][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:35.031][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 19:45:35.032][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:35.033][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 19:45:35.034][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:35.035][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 19:45:35.036][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-19 19:45:35.037][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 19:45:35.038][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:35.039][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-19 19:45:35.039][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 19:45:35.041][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:35.042][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:35.043][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 19:45:35.043][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 19:45:35.043][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 19:45:35.043][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-19 19:45:35.043][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-19 19:45:35.043][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 19:45:35.044][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:35.045][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:35.046][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 19:45:35.047][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:35.048][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:35.049][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 19:45:35.050][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:35.050][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 19:45:35.051][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 19:45:35.052][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:35.053][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:35.054][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-19 19:45:35.056][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:35.058][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-19 19:45:35.058][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:35.059][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 19:45:35.060][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:35.061][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 19:45:35.062][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:35.063][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 19:45:35.064][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-19 19:45:35.065][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 19:45:35.066][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:35.067][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-19 19:45:35.068][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 19:45:35.069][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:35.070][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:35.071][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:35.072][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 19:45:35.073][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:35.074][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:35.075][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 19:45:35.076][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:35.077][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:35.077][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 19:45:35.078][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:35.079][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 19:45:35.080][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 19:45:35.081][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:35.082][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:35.083][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-19 19:45:35.085][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:35.086][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-19 19:45:35.086][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:35.087][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 19:45:35.088][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:35.089][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 19:45:35.090][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:35.091][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 19:45:35.093][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-19 19:45:35.094][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 19:45:35.096][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:35.097][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-19 19:45:35.098][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 19:45:35.100][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:35.100][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:35.101][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:35.102][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 19:45:35.103][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:35.104][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:35.105][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 19:45:35.106][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:35.107][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:35.109][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 19:45:35.110][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:35.111][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 19:45:35.112][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 19:45:35.114][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:35.115][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:35.117][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 19:45:35.118][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.154][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[2025-03-19 19:45:35.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.175][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[2025-03-19 19:45:35.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.180][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[2025-03-19 19:45:35.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.197][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[2025-03-19 19:45:35.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.209][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-19 19:45:35.210][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-19 19:45:35.212][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-19 19:45:35.214][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-19 19:45:35.216][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-19 19:45:35.218][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-19 19:45:35.219][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-19 19:45:35.220][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-19 19:45:35.222][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-19 19:45:35.223][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-19 19:45:35.224][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-19 19:45:35.226][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-19 19:45:35.228][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-19 19:45:35.229][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-19 19:45:35.230][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-19 19:45:35.232][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-19 19:45:35.233][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-19 19:45:35.234][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-19 19:45:35.236][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-19 19:45:35.238][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-19 19:45:35.239][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-19 19:45:35.240][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-19 19:45:35.241][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-19 19:45:35.243][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-19 19:45:35.244][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-19 19:45:35.245][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-19 19:45:35.247][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-19 19:45:35.248][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-19 19:45:35.249][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-19 19:45:35.250][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-19 19:45:35.252][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-19 19:45:35.253][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-19 19:45:35.254][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-19 19:45:35.256][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-19 19:45:35.257][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-19 19:45:35.258][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-19 19:45:35.260][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-19 19:45:35.261][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-19 19:45:35.263][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-19 19:45:35.264][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-19 19:45:35.266][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-19 19:45:35.267][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-19 19:45:35.268][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-19 19:45:35.270][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-19 19:45:35.271][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-19 19:45:35.272][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-19 19:45:35.274][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-19 19:45:35.275][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-19 19:45:35.277][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-19 19:45:35.278][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-19 19:45:35.280][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-19 19:45:35.282][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-19 19:45:35.283][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-19 19:45:35.284][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-19 19:45:35.285][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-19 19:45:35.287][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-19 19:45:35.289][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-19 19:45:35.290][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-19 19:45:35.291][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-19 19:45:35.292][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-19 19:45:35.294][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-19 19:45:35.295][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-19 19:45:35.296][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-19 19:45:35.298][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-19 19:45:35.299][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-19 19:45:35.300][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-19 19:45:35.302][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-19 19:45:35.303][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-19 19:45:35.304][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-19 19:45:35.305][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-19 19:45:35.307][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-19 19:45:35.308][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-19 19:45:35.309][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-19 19:45:35.310][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-19 19:45:35.312][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-19 19:45:35.313][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-19 19:45:35.315][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-19 19:45:35.316][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-19 19:45:35.317][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-19 19:45:35.319][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-19 19:45:35.320][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-19 19:45:35.322][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-19 19:45:35.323][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-19 19:45:35.324][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-19 19:45:35.326][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-19 19:45:35.327][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 19:45:35.328][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.330][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.340][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.DEBUG[2025-03-19 19:45:35.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:35.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:35.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.346][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[2025-03-19 19:45:35.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:35.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:35.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:35.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:35.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:35.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:35.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:35.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:35.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:35.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:35.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:35.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:35.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:35.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:35.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:35.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:35.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:35.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:35.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:35.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:35.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:35.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:35.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.416][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[2025-03-19 19:45:35.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:35.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:35.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:35.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:35.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.429][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[2025-03-19 19:45:35.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:35.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:35.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:35.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:35.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:35.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:35.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:35.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:35.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:35.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:35.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:35.452][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-19 19:45:35.454][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-19 19:45:35.457][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:35.458][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-19 19:45:35.459][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:35.460][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 19:45:35.462][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:35.463][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 19:45:35.464][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:35.465][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-19 19:45:35.466][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-19 19:45:35.467][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 19:45:35.468][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:35.469][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-19 19:45:35.470][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 19:45:35.472][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-19 19:45:35.472][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-19 19:45:35.472][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-19 19:45:35.472][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-19 19:45:35.472][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-19 19:45:35.472][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-19 19:45:35.472][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-19 19:45:35.472][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-19 19:45:35.472][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-19 19:45:35.472][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-19 19:45:35.472][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-19 19:45:35.473][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:35.474][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 19:45:35.474][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 19:45:35.474][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 19:45:35.475][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-19 19:45:35.476][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:35.477][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:35.478][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 19:45:35.479][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:35.480][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:35.481][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 19:45:35.483][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:45:35.483][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-19 19:45:35.484][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 19:45:35.485][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 19:45:35.486][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:35.488][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-19 19:45:35.488][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-19 19:45:35.489][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-19 19:45:35.491][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-19 19:45:35.493][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-19 19:45:35.494][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-19 19:45:35.495][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-19 19:45:35.497][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-19 19:45:35.500][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-19 19:45:35.501][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-19 19:45:35.503][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-19 19:45:35.504][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-19 19:45:35.506][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-19 19:45:35.507][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-19 19:45:35.509][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-19 19:45:35.510][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-19 19:45:35.511][biodb::testThat]
biodb.INFO [2025-03-19 19:45:35.513][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-03-19 19:45:35.514][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:45:35.515][biodb::testThat]
biodb.DEBUG[2025-03-19 19:45:35.519][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-19 19:45:35.524][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:45:35.526][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-19 19:45:35.528][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:45:35.530][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-19 19:45:35.534][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:35.537][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:35.538][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:35.540][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-19 19:45:35.988][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-19 19:45:36.342][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:36.345][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-03-19 19:45:36.351][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-03-19 19:45:36.364][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-19 19:45:36.366][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-19 19:45:36.367][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-19 19:45:36.367][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-19 19:45:36.368][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:36.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:36.370][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.372][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-19 19:45:36.376][biodb::testContext]
biodb.INFO [2025-03-19 19:45:36.377][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-19 19:45:36.378][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-03-19 19:45:36.379][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-19 19:45:36.380][biodb::testContext]
biodb.INFO [2025-03-19 19:45:36.383][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-19 19:45:36.385][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-19 19:45:36.389][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 19:45:36.391][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-19 19:45:36.392][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-19 19:45:36.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.396][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-19 19:45:36.398][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-19 19:45:36.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.403][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-19 19:45:36.404][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-19 19:45:36.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.408][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-19 19:45:36.409][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-19 19:45:36.410][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-19 19:45:36.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.413][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-19 19:45:36.414][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-19 19:45:36.415][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-19 19:45:36.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.419][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-19 19:45:36.420][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-19 19:45:36.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.423][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-19 19:45:36.424][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-19 19:45:36.425][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-19 19:45:36.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.428][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-19 19:45:36.429][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-19 19:45:36.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.432][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-19 19:45:36.433][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-19 19:45:36.434][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-19 19:45:36.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.437][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-19 19:45:36.438][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-19 19:45:36.439][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-19 19:45:36.440][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-19 19:45:36.442][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-19 19:45:36.443][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-19 19:45:36.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.448][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-19 19:45:36.449][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-19 19:45:36.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.453][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-19 19:45:36.453][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-19 19:45:36.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.457][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-19 19:45:36.459][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-19 19:45:36.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.464][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-19 19:45:36.465][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-19 19:45:36.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.468][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-19 19:45:36.469][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-19 19:45:36.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.473][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-19 19:45:36.475][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-19 19:45:36.497][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-19 19:45:36.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.501][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-19 19:45:36.502][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-19 19:45:36.503][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-19 19:45:36.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.508][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-19 19:45:36.510][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:36.511][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-19 19:45:36.512][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:36.513][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 19:45:36.514][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:36.516][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 19:45:36.517][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:36.518][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 19:45:36.519][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-19 19:45:36.520][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 19:45:36.521][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:36.521][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-19 19:45:36.522][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 19:45:36.524][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:36.525][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:36.526][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 19:45:36.526][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 19:45:36.526][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 19:45:36.526][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-19 19:45:36.526][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-19 19:45:36.527][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 19:45:36.528][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:36.529][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:36.530][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 19:45:36.531][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:36.532][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:36.533][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 19:45:36.534][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:36.545][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 19:45:36.546][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 19:45:36.548][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:36.549][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:36.550][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-19 19:45:36.552][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:36.553][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-19 19:45:36.554][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:36.555][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 19:45:36.556][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:36.557][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 19:45:36.558][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:36.559][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 19:45:36.559][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-19 19:45:36.560][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 19:45:36.561][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:36.562][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-19 19:45:36.563][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 19:45:36.564][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:36.565][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:36.566][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 19:45:36.566][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 19:45:36.566][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 19:45:36.566][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-19 19:45:36.566][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-19 19:45:36.567][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 19:45:36.567][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:36.568][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:36.569][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 19:45:36.570][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:36.570][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:36.571][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 19:45:36.572][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:36.573][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 19:45:36.575][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 19:45:36.576][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:36.577][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:36.578][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-19 19:45:36.580][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:36.581][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-19 19:45:36.582][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:36.583][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 19:45:36.584][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:36.586][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 19:45:36.587][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:36.588][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 19:45:36.589][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-19 19:45:36.590][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 19:45:36.591][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:36.592][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-19 19:45:36.594][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 19:45:36.595][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:36.596][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:36.597][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:36.598][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 19:45:36.599][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:36.599][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:36.600][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 19:45:36.601][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:36.602][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:36.603][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 19:45:36.604][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:36.605][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 19:45:36.606][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 19:45:36.607][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:36.608][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:36.609][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-19 19:45:36.612][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:36.613][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-19 19:45:36.614][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:36.615][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 19:45:36.616][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:36.617][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 19:45:36.618][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:36.619][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 19:45:36.620][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-19 19:45:36.621][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 19:45:36.621][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:36.622][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-19 19:45:36.623][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 19:45:36.624][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:36.625][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:36.626][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:36.627][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 19:45:36.629][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:36.630][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:36.630][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 19:45:36.631][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:36.632][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:36.633][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 19:45:36.634][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:36.635][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 19:45:36.636][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 19:45:36.637][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:36.638][self$setPropertyValue]
biodb.DEBUG[2025-03-19 19:45:36.640][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 19:45:36.641][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.688][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[2025-03-19 19:45:36.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.722][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-19 19:45:36.724][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-19 19:45:36.725][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-19 19:45:36.727][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-19 19:45:36.729][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-19 19:45:36.730][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-19 19:45:36.732][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-19 19:45:36.733][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-19 19:45:36.735][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-19 19:45:36.736][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-19 19:45:36.737][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-19 19:45:36.739][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-19 19:45:36.740][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-19 19:45:36.742][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-19 19:45:36.743][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-19 19:45:36.744][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-19 19:45:36.747][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-19 19:45:36.749][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-19 19:45:36.751][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-19 19:45:36.753][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-19 19:45:36.755][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-19 19:45:36.757][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-19 19:45:36.758][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-19 19:45:36.760][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-19 19:45:36.762][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-19 19:45:36.764][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-19 19:45:36.765][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-19 19:45:36.767][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-19 19:45:36.768][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-19 19:45:36.769][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-19 19:45:36.770][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-19 19:45:36.772][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-19 19:45:36.773][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-19 19:45:36.774][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-19 19:45:36.775][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-19 19:45:36.776][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-19 19:45:36.778][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-19 19:45:36.779][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-19 19:45:36.780][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-19 19:45:36.781][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-19 19:45:36.783][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-19 19:45:36.784][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-19 19:45:36.785][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-19 19:45:36.787][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-19 19:45:36.789][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-19 19:45:36.790][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-19 19:45:36.792][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-19 19:45:36.793][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-19 19:45:36.795][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-19 19:45:36.797][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-19 19:45:36.798][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-19 19:45:36.800][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-19 19:45:36.801][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-19 19:45:36.802][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-19 19:45:36.804][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-19 19:45:36.805][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-19 19:45:36.807][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-19 19:45:36.808][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-19 19:45:36.810][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-19 19:45:36.812][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-19 19:45:36.814][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-19 19:45:36.816][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-19 19:45:36.817][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-19 19:45:36.819][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-19 19:45:36.820][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-19 19:45:36.821][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-19 19:45:36.823][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-19 19:45:36.824][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-19 19:45:36.826][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-19 19:45:36.827][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-19 19:45:36.829][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-19 19:45:36.831][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-19 19:45:36.833][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-19 19:45:36.834][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-19 19:45:36.836][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-19 19:45:36.838][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-19 19:45:36.839][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-19 19:45:36.840][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-19 19:45:36.841][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-19 19:45:36.842][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-19 19:45:36.844][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-19 19:45:36.845][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-19 19:45:36.846][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-19 19:45:36.848][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-19 19:45:36.850][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-19 19:45:36.852][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 19:45:36.853][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.855][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:36.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:36.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:36.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:36.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.867][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.DEBUG[2025-03-19 19:45:36.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:36.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:36.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:36.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:36.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:36.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:36.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:36.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:36.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:36.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:36.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.906][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[2025-03-19 19:45:36.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:36.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:36.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.912][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.DEBUG[2025-03-19 19:45:36.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:36.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:36.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:36.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:36.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:36.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:36.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:36.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:36.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:36.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:36.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:36.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:36.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:36.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:36.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:36.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:36.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 19:45:36.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:36.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:36.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:36.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:36.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:36.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:36.970][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-19 19:45:36.972][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-19 19:45:36.974][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:36.975][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-19 19:45:36.976][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:36.977][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 19:45:36.978][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:36.979][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 19:45:36.981][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:36.982][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-19 19:45:36.982][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-19 19:45:36.983][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 19:45:36.984][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:36.985][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-19 19:45:36.986][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 19:45:36.987][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-19 19:45:36.987][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-19 19:45:36.987][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-19 19:45:36.987][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-19 19:45:36.987][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-19 19:45:36.987][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-19 19:45:36.987][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-19 19:45:36.987][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-19 19:45:36.987][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-19 19:45:36.987][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-19 19:45:36.987][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-19 19:45:36.989][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-19 19:45:36.990][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 19:45:36.990][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 19:45:36.990][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 19:45:36.991][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-19 19:45:36.992][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:36.993][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:36.993][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 19:45:36.995][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 19:45:36.996][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 19:45:36.997][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 19:45:36.998][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:45:36.998][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-19 19:45:36.999][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 19:45:37.000][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 19:45:37.001][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-19 19:45:37.001][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-19 19:45:37.001][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-19 19:45:37.003][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-19 19:45:37.004][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-19 19:45:37.005][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-19 19:45:37.007][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-19 19:45:37.009][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-19 19:45:37.011][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-19 19:45:37.014][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-19 19:45:37.015][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-19 19:45:37.017][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-19 19:45:37.018][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-19 19:45:37.019][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-19 19:45:37.020][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-19 19:45:37.021][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-19 19:45:37.022][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-19 19:45:37.023][biodb::testThat]
biodb.INFO [2025-03-19 19:45:37.024][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-03-19 19:45:37.025][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 19:45:37.026][biodb::testThat]
biodb.DEBUG[2025-03-19 19:45:37.029][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-19 19:45:37.033][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:45:37.040][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-19 19:45:37.042][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:45:37.044][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-19 19:45:37.048][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-19 19:45:37.052][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 19:45:37.054][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-03-19 19:45:37.055][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 19:45:37.056][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-03-19 19:45:37.061][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-03-19 19:45:37.062][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 19:45:37.063][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-03-19 19:45:37.065][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 19:45:37.066][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 19:45:37.067][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 19:45:37.068][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 19:45:37.069][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 19:45:37.070][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 19:45:37.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:37.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:37.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:37.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:37.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:37.083][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:37.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 19:45:37.086][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-03-19 19:45:37.088][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 19:45:37.090][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 19:45:37.091][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-03-19 19:45:37.473][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-03-19 19:45:38.509][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 19:45:38.512][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-03-19 19:45:38.518][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-03-19 19:45:38.522][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-03-19 19:45:38.525][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 19:45:38.527][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 19:45:38.528][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 19:45:38.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 19:45:38.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:38.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:38.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:38.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:38.542][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:38.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 19:45:38.550][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:38.552][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:38.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.555][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:38.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:38.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.562][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:38.563][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:38.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.566][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.568][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 19:45:38.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 19:45:38.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.572][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:38.573][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:38.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.575][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.577][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 19:45:38.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 19:45:38.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.581][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 19:45:38.582][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 19:45:38.584][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.585][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.587][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 19:45:38.588][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 19:45:38.589][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.590][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.592][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:38.593][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:38.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.595][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.596][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:38.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 19:45:38.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.602][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:38.603][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:38.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.605][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.607][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 19:45:38.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 19:45:38.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.612][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:38.612][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:38.613][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.614][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.616][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:38.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 19:45:38.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.619][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:38.620][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:38.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.622][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.624][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 19:45:38.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 19:45:38.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.630][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:38.631][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:38.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.634][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.636][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 19:45:38.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 19:45:38.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.641][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:38.642][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:38.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.644][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.646][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 19:45:38.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 19:45:38.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.651][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:38.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:38.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:38.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:38.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:38.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:38.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 19:45:38.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 19:45:38.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:38.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:38.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:38.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:38.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:38.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:38.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:38.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:38.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:38.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:38.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 19:45:38.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 19:45:38.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 19:45:38.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 19:45:38.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 19:45:38.693][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-03-19 19:45:38.698][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-19 19:45:38.699][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-19 19:45:38.700][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-19 19:45:38.701][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-19 19:45:38.701][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 19:45:38.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 19:45:38.715][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 19:45:38.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 19:45:38.717][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 19:45:38.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
>
> proc.time()
user system elapsed
19.915 1.249 57.973
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 2.490 | 0.951 | 4.696 | |
| ChebiEntry | 0.320 | 0.015 | 0.345 | |